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

Are you referring to the 2 bolts that go in from the bottom of tensioner itself? Not either of the round pulleys? It looks like the pulley for the tensioner takes a 10mm Hex wrench. But there is nothing that says anything is opposite thread.

The bolt holes look to be part of the oil pump assembly, but there isn't any place that states one bolt would be reverse thread, I supposed it could be an aftermarket oil pump, but that still doesn't make much sense of a design. But since those bolts are straight up and down, drilling one out should be easier. But there isn't any close up pictures of the tensioner bolts.

Just going over your pictures here close up, so is it the bolt hole closest to the engine block that broke? Comparing the 2 bolts it's hard to tell what thread they are with so much missing off of that one. So, from the bottom up, you're saying the front bolt hole doesn't tighten turning it to the right? I've been going through service info and have not seen anything like that. Considering what it holds, you would think that would be something specifically noted in there. It still looks like a tough one to drill out, but if you can get a smaller bit started first so you have a pilot hole to keep the next bit straight is what I would try. By the time you get the center of that drilled out, there won't be much of the bolt left. I can see how small it is compared to the other bolts in the block. Looks like maybe a 10mm. But as for the thread direction right now, I would just try to get started with a small bit and take it from there, You don't want to damage anything, Such a bad design. I would expect more from Toyota, but anyway. Zoomed in the bolts look like the end thread is correct being tightened to the right, even the full one on the left, I have the picture straight up and down, if I were to twist either of those, I'd need to go right to thread it in. If you have a nut that will fit on there, that would give you a clear answer, The way those threads are at an angle down on the left side, now I'm looking for a bolt here. On normal right-hand tightening, the threads will be angled down on the left side. I'm trying to post a picture for you here. I'm not sure if it's the picture or not, but the broken bolt looks a little different, that might just the picture though.
Granted this is just a screw but it's the correct thread, just a bit easier to see, but how the threads are angled down on the left side, that's what I see, at least that's what I think I see on the unbroken bolt.
You won't tighten that bolt anymore, the broken section must be rusted in there, drilling out the center will reveal some of that. Then just increase bit size until you can get an easy out in there, or it starts to move. Spray something for the rust while doing it, some penetrating oil, which will help to save the bit too, but drill slow, if you go too fast with drilling out metal bolts, you'll just burn the bits up quick.

Well, it looks like it would just spin out the top, isn't there a hole at the top of those threaded areas? But I think you have a good plan. If you keep spraying each day until you get to drilling it that will help a lot, letting it soak overnight each time. Hope it goes well, if it happens to be reverse thread, let me know, I'll send a message to All Data, maybe they will correct the service info.

Well, with the towing strap, the only way to know is to do a pressure test, you might find that it hit the radiator fins and cracked something in that area, they are pretty fragile. But you can rent a coolant system pressure kit from AutoZone, or other places might rent tools as well. The kit comes with different fittings for radiators and a pump with a gauge on it. So, you just fill up the system, pump it up to about 15psi, I believe the max you want to go on a cooling system is 18psi, but 15 is usually enough to find a leak. That is about where the system will be when it's up to operating temperature. Thats unfortunate about the tensioner bolt. I don't think that will hold for very long, the pressure on the tensioner is pretty high, but I think changing the oil pump out is the only way to remedy that situation now. I can't think of any other way to secure that other side. I hope for the best though. For the pressure test you can use water, you'll just need to drain it out later and add 50/50.

The tow strap might have just hit a coolant hose, it's difficult to tell until it's under some pressure. The Permatex was a good idea, that stuff can handle quite a bit. I was also thinking about the hole you drilled in the side. Since that hole is not part of the actual engine block, and only the oil pump, (meaning it can be replaced in the future) you could try a self-tapping screw and see if it will help put some support on that underside where the broken bolt should be. If you can find that right size self-tapping screw. I know it's kind of a hack, but at this point if you're not planning on keeping the van that much longer. Just trying to think of anything you can do besides replace the oil pump. I know you just want to get this thing done. And btw on the tool rental at AutoZone, its actually free, you just have to give them the money in case you don't return the tool. Once you return it, they give you all your money back. As long as it's not damaged obviously. But I forgot to tell you that part.

I was just thinking a small self-tapping screw in the hole you already drilled, or whatever you think will help secure it or at least help hold the tensioner a bit more. Did a bolt break on the new water pump? It really depends on what you can fit into the area of the broken section on the bolt. I try to get them out by soaking it in penetrating oil over night and drill, then try to get an extractor in the drilled hole. Some kits actually come with a drill bit that drills in the opposite way, then using a regular drill bit to try to spin what's left of the bolt out. There is never an easy way, especially when space is limited.
This video might help, he uses some techniques with a hammer and punch on the edge of a broken bolt in an engine block, might be helpful somewhat. I hope.

https://www.youtube.com/watch?v=x_ky5JVxtqU

Okay, I see what happened, yes considering how far you are along with the job, if that bolt was threaded into the water pump as well as into the block, which would be a difficult one to get out. With older higher mileage vehicles, a lot of things tend to break. I do hope everything holds up for as long as you keep the vehicle. And in this industry every job seems to be a learning experience.

Do you have both of the power steering pump bolts free enough to move and adjust the pump position? The Harmonic balancer should really only seat in one position. I would put the belt on the crank first then the PS pump last. The lower bolt on the pump is the adjusting bolt.