On starting up, the game tries to create the Mod and Save directories inside the game directory and continues to write save data there. If the user lacks permission to do this, the main menu never appears. Why would the user lack permission? Well...
I'm the Gentoo Linux games team lead and I'd like to add this game to our repository. This would give you added exposure. It would be involve users downloading the purchased zip from here, sticking it in a folder, and the package manager would install it system-wide with a menu icon and so on.
That doesn't work when the save data is written to the system-wide location. Where should it go? There are already a couple of files, prefs and Player.log, written to ~/.config/unity3d/Fractal Phase/Sky Rogue, and it should live alongside these. I had the same issue with Assault Android Cactus+, which is also Unity-based, and the developers were kind enough to fix it for me. Please could you do the same? Working around this some other way is so painful that I don't think I'd bother packaging the game at all, which would be a shame.