Hi
I use the steam version with some mods, and I do not experience any problems (other that I would have with DVD installation).
First, in steam you can move your installation folder in options. You can have a special folder just for one game.
Second, I think you can copy the SH3 folder in different place -- at game launch it will verify that steam is running and the game is in your library.
Third, I don't see problems modding in steam folder, but you should keep backups in some way. Probably it better to have in separate one. If you do not ask to verify the cache, steam will not do it for you and will not rolldown to initial state. But if there some updates, steam will forces them (thanks Rockstar!).
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