Wine ARB + SB = 32.24 FPS = 49% improvement
So faster again, but very minor graphical glitches from what I can tell. Keep in mind there may be engine differences as well. Perhaps the Linux version is using a newer version of the HL2 engine, although graphically they don't look dramatically different.
EDIT: Upon closer investigation, I do think that the Linux version is using a newer engine. I believe that it is actually using HDR for one, whereas the older engine just reports but doesn't use it.
So I disabled HDR, Bloom and motion blur, and ran it again:
Native Linux SB = 30.66 FPS
That might not be enough for it to be comparable, however. I think we'll have to wait for the new engine to make it into the Windows version for these to be directly comparable. But yeah, the engine differences limit these results, obviously. Probably should have checked more closely in the first place.