The games steam version for linux uses wine already.
I don't know how steam games are made & set up, so this is all hypothetical.
From what I can gleam of the game on linux, there are two scripts added:
Xenonauts/detect_wine
Installs wine using distribution specific packagemanagers.
Xenonauts/usr/bin/xenonauts
Checks if wine exists and if it does, calls 'which wine xenonauts/Xenonauts.exe'.
I'm guessing the later is what runs the game on linux?
Maybe Goldhawk could tell us how they setup the linux version so CE could do the same?