Is this normal for a crankshaft on a 1MZ-FE engine?

Hello, it looks like you have it correct. The mark on rear trigger wheel looks lined up. Will post service info showing the correct marks for the crankshaft and the camshafts. If you clean up the area on the engine block where it says Toyota, the mark will be easier to see.
Just make sure when putting the new belt on that you get any slack in the belt on the side/area where the tensioner is, so the tensioner takes up the slack and none of the cams move.
A trick that can help is when you have the timing belt marks lined up on each cam with the mark on the belt, using tie wraps to temporarily hold the belt on the camshaft sprockets helps a lot. Are you replacing the tensioner or idler pulleys? And need the torque specs for either?
That small mark on the front crankshaft gear is to line up with the timing belt line as seen in the 3rd diagram. It shows all the timing marks. Here's the torque specs for the water pump. 4th diagram.
Here are the rest of the timing belt installation specs and details.

The 1st and 4th picture are your crankshaft gear correct? And the 3rd looks like one showing where the mark is supposed to be lined up. When you say upper and low teeth of the gear, what kind of difference are you seeing? They look fine to me from what I can see in the pictures. Is there something wrong with the lower teeth that is not visible in the photos?
Unless you're referring to the photo with the arrows pointing to the mark on trigger wheel and the crankshaft at TDC.

All the 1998 Sienna's have the 3.0liter 1MZ-FE engine, even all 3 sub models CE, LE, XLE. That posting is all over the place, The small mark on the trigger wheel for the crankshaft position sensor is where it should be, lined up with that hump you have circled. The marks on the timing belt are there to get everything where it should be after releasing the tensioner. With the 3 timing marks, (1 on the crank, and 1 on each cam, ) the number 1 piston is at Top Dead Center on its compression stroke. Once the belt is on and everything is lined up, the tensioner is released, you rotate the crankshaft 2 rotations, and recheck the camshaft marks, they should be lined back up. That whole post on that forum looks to be confusing people more than anything. These are all 3 timing marks. There is no other engine for this year listed in the service info. All 3 sub models have the same timing marks, same engine. 1998 is the first year the Sienna is listed, there isn't anything for 97'.

Once you get the timing cover back on and the harmonic balancer back on, then the crankshaft bolt in, the crankshaft gear will be held in place by the rest of that. This is a diagram of the belt guide.

It looks like that back timing cover is supposed to come off for access to the water pump, but there's something to think about, if that camshaft bolt breaks off, for whatever reason it is going to open up a whole new can of worms. I've had cam bolts that would never come out, even on a brand-new cylinder head. I've had the cam holder tools break on me. So, if you think the water pump has been done already and it's not leaking. I would leave it. Unless you can get one cam sprocket off and get behind the back timing cover, semi out of the way, I'm not sure how much room that would give you. But you don't want to break the cam bolt's head off. That would leave you having to drill it out or more likely have to replace the cam. The cam bolts are not as strong as the crankshaft bolt. I just don't want to see you in a situation that can go from bad to really bad. It looks like the drive side cam is 94ft lbs torque and only 65ft lbs for the other cam.
It's possible that the engine has been apart before, and that's why you're having to fight with bolts. Trying an air impact gun might work, but a breaker bar is how it will break off. 94ft lbs isn't so much, you should be able to do that by hand. Just be careful.

Yeah, I would definitely tighten up the bolts and 2 nuts for the water pump if they're loose. That tells me that someone else has been in there already and obviously didn't torque things to spec. That would explain why the cam bolt is so tight too. But instead of taking a chance of breaking that cam bolt. Tighten up the water pump bolts, here's the spec on them, it is the 4 bolts and 2 nuts, and the torque spec only being 53in lbs, so it's not that tight at all. The real test to see if it will leak is to either put it all back together and run it and the coolant system will pressurize when it gets up to operating temperature. Or Auto Zone and other auto parts stores actually rent out tools, so you could rent a coolant pressure test kit and pressurize the system up to about 15psi and see if it leaks that way, that is about the max you want to get the pressure up to. Any more than that and you risk the heater core leaking or hoses. So, you could do it that way, that will prevent you having to take the whole thing apart again if it does happen to leak. The coolant pressure kit is just a pump that hooks onto the radiator cap opening, or reservoir, wherever you fill the coolant. And it has a pressure gauge on it. You just pump it up the 15psi and check for leaks. It has different fittings for different vehicles. That is probably your best option. The bolts for the water pump can come loose from normal engine vibration, especially if they were not torqued correctly to begin with. Then if the pump does leak, take things from that point. Is it the driver side cam bolt that is giving you the trouble?

https://www.2carpros.com/articles/radiator-pressure-test

https://www.2carpros.com/articles/car-is-leaking-coolant

Yeah, that's looks like the weep hole, the internal seal must have failed. I see that cam is on Bank 2 towards the front of the vehicle, that is the one that is torqued to 94ft lbs. It looks like that number 3 timing cover is the rear one, they should have designed it differently. Having to remove the cam sprockets to get a water pump out seems extreme. If that cam bolt starts to move, try spraying something behind the cam sprocket onto the whatever section of the bolt that might be exposed, if you can get something on the threads it will help.

Yeah, the entire rear timing cover needs to come out, considering most of the water pump is exposed already, their design is frustrating. I know how difficult some of these can be. Hopefully things go okay for you. I'm not sure if you have the valve covers off, but there might be something more to hold on to under the valve cover. Some camshafts have square sections where you can get an open-end wrench on the camshaft for a better hold. I'll look through service info some more for you and see if there's anything else helpful. It's not clear if there are square sections on these cams, I'm looking for some parts images.

I can see the gasket; did you get a new one yet? It will come with a gasket, just be sure to clean the mounting surfaces off really good, and don't get any oil on the new gasket. Torque spec is 53in lbs for the water pump bolts and nuts. Check that there isn't any coolant in the oil before starting the vehicle too.

Was it the number 2 idler pulley in the diagram, the upper one with the center bolt? It's difficult tell you without really seeing how much room you have, which I'm sure is not much because of the engine being sideways in the engine compartment. Unfortunately, service info has the engine being lowered out the bottom with much of the sub frame being removed along with the suspension. I'm not sure if it's possible, but if you can angle the engine up on the left side to be able to drill that bolt out. Most engines do come out when bolts like that break. I only thing I can think of is using a 90degree air ratchet to try drilling it out. Pulling this engine is more work than you want to get into. Plus, it looks like you'll need a lift to do it as well. Real sorry this happened, it was a worry from the beginning.