(ie: no need for doors on any shops other than butchers and tanners to keep miasma from spreading if you accidentll leave out dead animal skins)
What about strange moods?
Treat those like the butcheries. If the design's expandable then doors can go anywhere, yes?
Tweak (Gibbed's 1.3.0.0, if there are multiple versions around) will restore natural walls, you just need to find a natural wall of the sort you want and then use it as a template. Since the geo and layer layers are going to be already correct if you're restoring walls rather than creating them out of nothing, all you need to do is change the type so that the tile is a wall, a floor with a ., a floor with a ', an up stair, etc.
These values are all correct for the layer stone of the relevant tile. Clusters and veins are sort of 'painted on' to the underlying layer stone, and building a construction on clusters and veins removes this 'paint'. This is not determined directly by the [LAYER] tag, but by the geography of your site. (In vanilla, this only applies to the obsidian around the top of a magma pipe, and probably any obsidian floor you make yourself out of the pipe's obsidian.)
Rough wall: DB 00
Rough floor: 50 01, 51 01, 53 01
Up stair: 39 00
Down stair: 38 00
Up / Down stair: 37 00
Up ramp: ED 00
Down ramp: 01 00
Rough wall, special: B8 01
By 'special', I mean 'whatever was on that tile immediately before you Tweaked it'. Layer stone, cluster stone, ore, gems...
I don't have the type values for anything other than a wall, but you don't need 'em anyway except to save time.