For testing purposes i have installed ubuntu 15.04 with Wine 1.7.42 and tried to see what works and what not:
Vannila FL: Installs, works.
FLMM: Installs, works, applies the mod correctly.
CF 2.0: Installs, Launcher updates correctly. Shorly before initializing the game an error "Freelancer.exe not found" is shown depite the .exe is there.
If anyone has ideas how to solve this, i would appreciate it.