I never used Unity engine, but I though for simply scripted games within its environment the mac/linux builds are one click away, just like the win builds.
So if takes that much effort just to try to build it, you are already using some kind of more complex setup, beyond simple scripts of Unity (no real surprise, quite opposite, it’s hard to believe some generic engine is mature enough to be able to script a game of Ascendant kind).
Still makes me curious what’s blocking you, pure portable C++ should not (the C++ OSS compilers are generally better that MSCC now, so I would even recommend to try them for win builds), C# is beyond my experience, but looks like Mono is quite usable for many games (but definitely needs testing during development, to not use some windows-only C# solution).
The graphics API and stuff is still major pain with all the different distros and subsystems, but you should be shielded from that by Unity.
Well… in case you are hitting problem already with something I mentioned, maybe try to somewhat describe it, there are probably users (including me) with some SW development background, capable to give some advice here and there. Although these things tend to be quite specific and stubborn.
But I’m afraid you are already entangled in some other non-standard stuff…