No, Windows is naitive, Linux is just an - obviously less efficient port.
All servers running Linux (JgKdo, FOOL, n1) can host significantly less players/smaller maps than the windows servers (Odie, Shan, 121st) with similar hardware.
The current DTAS setup for INFGermany (although nothing else runs on the machine: no TS, no forum, no webside, no other game, no file redirect, no email client) can't run any of the BP maps (except for Tusacany night) and several of the 2.9 maps (Bordertown, Ruins - not even Kososvo or Macedonia) on an Athlon XP 3000 (+1 Gig Ram) with a humble playerlimit of 14 (unless you accept a pingrise of 150 for everybody once server is full) - which is a real shame looking at maps like Bocage, The Raid, Pueblo or Dullrocks II. Ancient map Remagen caused a tickrate drop from 25 (=CPU Power sufficient) to 13 with 10 Players on the server... which is unplayable and means you'd need twice the CPU power.
I searched the web and I ran in to a few post that confirmed exactly that (for original UT and TO - rule of the thumb: windows = 4 players more can be handled) but I couldn't find any real benchmarks Linux vs. Windows. We already considered migrating or trying to gain performance with custom kernel but it's lots of work and means quites some downtime....