for the tilesheets, im pretty sure they have the same number of tiles, so i guess its a matter of prefference. but its also easier to make and easier to use and understand. if you look at the picture i showed you can see the diffrences in production, so i thinkk its easier to produce uniform tiles of the same size so you dont get those diffrences in production.
im having a look at the water tile. its err, not optimal. for this node, you want to do like you do with the ordinary tileset where you have items and trees and such. this is not an "animated sprite" tile, this is a tilemap, if you brake it of like you do with sprites, you cant animate them in godot (if you can, i dont know how) see, the way the animation works is that you mark the first in the set, pick it, then add "frames", the frames move in a lateral direction, so if it brakes of, the frames wont add, its a dead end so you cant animate it.
I made another video showing the proces, i hope the videos help xD
i havent tested the new autotiles but from looking at them i can see that the nr 2 is better than nr 1, but i can see the use of both. however i wouldnt use the one with thick lines for autotiling personaly, but i can see its use in making thicker lines of grass :)