I try to answer at least from my perspective
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1. I dont need it, but for minor things itd be a nice add (im not thinking of building rooms above rooms, but just using it for small intersections like streams under the bridges and stuff like that, really a 2 faces overlap like in my tests) also, testing this will be fun!
2. alignment depends of what you need. if you use the switch, it can be done automatically by using door nodes, so a door instead of a placeable, that snaps so no toolset placement issue,
if you use placeables, like helvene's beds or otr holes, i think its tricky, 1st you need to match the tile geometry to fit the placeable one. so if you want to make a walkable table, 1x2, you need to make in the tile a geometry that fits this, so yes, its easier to make tiles instead... if we dont find a way to fool the engine!
2b. agreed
2c. agreed
3. for me, more of the overlapping thing, that i dont think it can be fooled, no matter how we try, we can just use that placeable/door thing to get a switch, and that also needs tests because i havent done them... I was saying, more of that, Id be interested in seeing if we can tweak the code to modify some materials, and get for example, the chance to use different grass types. thatd be a great improvement, and I dont think it would bring bugs with him. its just material substitution, if it can be done...