I know how to trim a document to get rid of surrounding transparent space, but is there a way to do this only for saving off to web & devices, without impacting the actual document?
Solution A: Duplicate Image
When you want to save a web copy, you could duplicate the image (Image -> Duplicate), then do the adjustments for the copied (and possibly flattened) image.
I usually do it that way so the original image stays untouched, while the web save gets little color tweaks and watermarks. After saving I discard the copy, since there's really no need for it.
Solution B: Slices
You could also use Slices for this.
Personally I think it's a bit clunky way to do it, since it likes to create extra folders, and slices get in the way on the image side. But maybe it'll work with your work flow.