So I think you're talking about giving each biome a layer and stacking them on top of each other. That works for 98% of scenarios. But any time you have a section of width/height 1 tile, you run the risk of covering it up by another layer. (at least in a 2x2 bitmask, may not be an issue in a 3x3. ) I did that for the longest time, until I started noticing small peninsula's and bays in my ocean were appearing/disappearing where my code said there wasn't one. Place a single random tile of iceland in the dirtland and depending on how you layer things, it can vanish entirely.
I have my auto tiling working pretty damn well at the moment. lacks a buttload of polish, but it even wraps around. The ultimate goal I'm trying to do is be able to "lock" tiles into place and then reroll the world around them. I haven't actually tried exporting something in godot yet but I bet I could throw something up in github once I figure it out.
If people are interested