Well for starters, MV/MZ's animated tiles (Such as water and waterfalls for example) only have 3 frames, but it's possible to squeeze out 4 frame animation by formatting an object as a "character" and setting up a move route that turns it in the four different directions (up, left, right, down). Although, to make animations beginner friendly, keeping to the 3 frame auto-tile format is probably best for most objects.
When it comes to furniture and objects meant to be placed along walls I think it's best to center them vertically on 3 tiles even if the object only takes up 2 tiles. reason being is that it'll look much better (like it's up against the wall), but this is assuming that there is enough space to do so in the B~E tile sheets. There are scripts that can do the same thing without "wasting" precious space in your tile sheets, but you'd have to assume not everyone would be using those.
When it comes to the Vx/MV/MZ, the auto-tile format is pretty bad. It's very compact, and therefore you sometimes have to crop more complex patterns for it to work. As a workaround, it is possible to use the A5 tile sheet for more complex patterns if they're difficult or impossible to fit into the auto-tile format, as these tiles are drawn on the same layer. But the A5 sheet is pretty small and placing tiles there will make them normal tiles, not auto-tiles. It is an option you have though for certain ground/wall patterns.
As for how the MV/MZ auto tiles work. Here's some resources that should explain it :
Official RPG maker blog: https://www.rpgmakerweb.com/blog/classic-tutorial-how-autotiles-work
Random YouTube video (~30min) explaing the VxAce format (it's the same as in later engines):