Tansmission or transfer case

That would be an extra bolt hole that is used in other applications that use that engine. Not used with the combination that you have. Nothing to worry about.

Nope. The case is built to accept a few different transmissions. Some use that bolt hole, the automatic you have does not use it so it stays open. Now if you had the manual transmission it would have a bolt in it because that transmission bell housing uses that bolt. There is no possible way to make that part flush with your transmission because you would need to break the casting, move it, weld it back together and drill a hole for the bolt.

That is a reinforcing rib at the edge of the case, if you could see inside there is another one that lines up with the inside of the case you have. Here are a couple examples to show it's normal.

No bolt missing there either. GM makes many of these parts to fit into multiple vehicles and applications. They drill and tap all the holes simply because it's faster and easier and makes it so that you can add or subtract the various parts and brackets to fit the vehicle and options it has without needing special parts.

That way they don't have an engine block that can only be used in a 2001 Chevy P/U without AC but with power steering and an automatic transmission. But won't fit the same block if used with a manual transmission.

Instead the same block can be used in the entire truck and car line and everything bolts up as needed. Doesn't matter if it's an automatic or a stick shift or if it has a hydraulic or cable clutch. The holes are already there.

In this case that hole isn't used with an automatic transmission. It's just there. Start looking and you will also find many more holes and wires and even brackets and studs that are empty or lead to nothing. It's just cheaper and faster to make the parts that way at the factory to fit all the possible configurations.

For instance that same 4.3 block is used in the P/Us, Vans, S-Series, Boats, and industrial applications. Same thing with the transmissions and other parts.

Then the rear main seal around the crankshaft is leaking. It is in the back of the engine directly above that area. The oil drips out of the seal gets thrown around by the face of the torque converter and finally collects at the lowest point, which is just above that spot.
The other leak can be the torque converter pump seal, it is on the opposite side of the torque converter in line with the rear main seal. It can also leak and get thrown around and will drip out in the same place.
The most common thing would be slight leakage from both. Especially with that many miles on the truck. To repair it the transmission and transfer case are removed, Then the rear main seal gets pulled and replaced and the front pump seal gets replaced and you bolt it back together.