Doesn't the GTS have carbon fiber trim? Not sure if it is on the console though. But if it is, perhaps you could convince the right person at BMW to ship you that part.
Although depending on what you meant by "the knob gap is wider" that might still be an issue. Does that refer to IDrive? GTS doesn't have IDrive obviously, but even if it did, I didn't realize there was a difference between the IDrive cut-out for M3 vs. 3 series. Anyway, even if you have to mod that part slightly, at least you don't have to worry about the button cut-outs, which seems to me would be the toughest part to get right.
2008 Interlagos Blue E93 M3 - M-DCT
2011 Salsa Red Jetta TDI Sportwagen - DSG