I just compiled your xmega65.native on Debian Stretch.
As far as I can see, it works well. Altough I have one remark: I miss the "make install" which should move the binary in /usr/bin (p.e.) and the needed support files (ROM,char etc.) in /usr/share/xmega65 (p.e.).
For now I'm looking (aka searching) for docs. For xmega65 (keybindings etc) as well as for the mega65 (c65), especialy of course for the basic and how to change graphics mode etc. I guess the monitor is the same as those from c16/116/+4 and c128.
Btw. Great job you did LGB, I really appreciate your work. Puts me 36 years back in times when I still hat some hair covering my brain ;)