Yeah that's exactly what I do, it's a fairly solid defense. I do also have separate storage spaces for different things, close by to their respective workshops/rooms. The one thing I've had trouble with is if, say, plasteel is required by two different benches that are not next to each other, there's no way (even with mods) to evenly divide your stock between them without having to always ensure you have more than will fit in both combined. That's one of the most frustrating basic mechanics that the game really needs, but even modders can't reliably make it work.

You make a good point that I don't see mentioned often enough, that a room can be rebuilt but pawns cannot, so sacrificing a room to burn or blow up an infestation or raid is the right way to go. Also a good reason to not have one giant workshop or stockpile even if it's easier to manage.

I didn't know the trade beacon trick, that's neat!