Based on an earlier thread from a linux user seeking the CD VERSION configuration tool to enable directdraw/software rendering and my own experience trying to run the GOG version under Crossover Games (a prettied up mac version of wine) I would have to say at the moment, not brilliantly.
Myself, I get graphic bleeds (mouse trails, then if you actually try to walk every pixel bleeds (like going through a Doctor Who tunnel). In the earlier thread about the old config tool a developer from GOG basically suggests avoiding the other rendering modes (with the newer GOG version) for fear of greater bugs showing up.
Unfortunately software rendering is the only commonly recommended method for getting the CD VERSION to run in wine/crossover games and the same seems to be true for the GOG version.
I do own the CD VERSION and have managed to locate the old configuration tool on disc 3 but to my shame I haven't tried using it myself with the GOG version I bought 2 days ago. I hear it does work with the GOG version (again, from that earlier thread), but I cannot offer personal advice or horror stories yet. I just dual boot which isn't exactly an elegant solution.
What I should have posted first up:
http://www.gog.com/en/forum/divine_divinity_series/how_to_change_the_rendering_engine That old thread, the CD VERSION config tool seems to be working for at least a couple of people, so far. So the moral of the story is, unless you can get ahold of the old configuration tool, and are willing to put up with whatever bugs software rendering throws your way, avoid the new version if your only method of play is wine/crossover.