You are already using the same techniques that I would use on existing polys.

However, it is possible to 'square' a corner in an existing smooth polygon by adding a second node directly on top of an existing one. That's a little tricky to do, though.

A wise move - making separate copies to do anything experimental on.

Sinister Sewers doesn't use the usual wall cutting tools, so I think you would be all right doing that - as long as you realise it would become quite difficult to separate entities by layer. You would have to separate them by sheet instead.

However, to separate the levels you might wish to have separate sets of sheets instead of layers, so you can cast a shadow (for example) on the lower levels from the upper ones. Layers don't give you that power.

Ah, yeah. Western style, but not really the right scale.

Nice work! :D