Nah, it's not a silly question. :) There shouldn't be any problems if they're all in the same game. Some tilesets are tinted to have a certain mood (like the swamp or the haunted house), so they probably won't mix as well with other tilesets on the same map, but are ok if separate. There are a few older ones that are in the process of getting new versions to make them match better as well.
Kokoro Reflections
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Sure! If you've seen RPG Maker default tiles, they're much the same as those, with similar biomes. Grassland, sea, desert, snow, and mountain areas mostly. They're in PNG format and they include a non-RPG Maker version that should work for you in Godot. Having said that, though, I have no idea how usable they are for procedural generation. This tileset will be getting an update in the near future as some of the art is inconsistent with the style of our newer tilesets, so that's something to keep in mind as well.
For the Tuscan set, the version on Steam is v2. For sample maps, check here: https://kokororeflections.com/product/sample-maps/ Hope this helps.
Yeah, you will want to add that using an overlay plugin like Galv's. I think Cyclone Engine can do it too.
For the town, we don't have anything for this exact purpose yet. We checked over our list of existing tilesets and the closest thing we could find was the Sun/Moon Palace, the orange Sun version, if darkened slightly, seems to work pretty well colorwise, but the imagery is all wrong. It would be pretty limited.