Hi - the tricky thing with the transparency tiles is that it would require you to make 1 terrain layer per "type"; As far as i know, in GODOT, one tile cannot contain more than 1 texture - so you'd need a grass layer and a stone floor layer. This can begin to get complicated quickly.
For my project, I found it easier to have 1 "floor" layer and define the transitions as per your non-transparent textures. Then the next layer is "walls" (for "blocking" tiles) and then another for "props" (like trees, lamp posts or chests).
I tried the transparency layers approach and it became tricky with things like z-indexing and y-indexing when moving around. There is almost certainly a better solution than mine, but I found a simple "floor" layer easier to work with.
TLDR: please don't take away the predefined transition terrain sections ;)