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They support all of that. At my last job, we made a huge 3d facebook game written entirely in c#. We compiled independent libraries, copied them into Assets/Plugins and ran the game using the UI. Everything was procedurally generated because, back then, we had some serious issues with missing texture references. The best part is, because compiling c# libraries has nothing to do with Unity (other than including the Unity libs), it can be done using a variety of methods and IDEs.

We started the project without knowing if the compile to flash target would be done when we needed it, so we hedged our bets and kept unity as separate from the game code as possible.

The downside is step through debugging can only be done with UnityVS or MonoDevelop and you don't get the flexibility of using "that complex UI", which I rather enjoyed using as a REPL. Oh, going from code change to compiled to seeing the game on the screen was sloooooooow.