The server appears to exec some files meant only for clients - a couple warnings i saw:

execing xonotic-client.cfg
Warning: Could not expand $vid_width
Warning: Could not expand $vid_height
Warning: Could not expand $vid_pixelheight
Warning: Could not expand $vid_desktopfullscreen

execing commands.cfg
Warning: Could not expand $qport in alias _if_dedicated

couldn't exec config.cfg

execing font-xolonium.cfg
Warning: Could not expand $scr_loadingscreen_barheight
Warning: Could not expand $scr_infobar_height
This command only works on clients: cl_cmd hud scoreboard_columns_set

A couple more things that would be nice to get rid of:

FS_OpenVirtualFile("data/maps/.mapinfo", false): nasty filename rejected
FS_OpenVirtualFile("maps/.mapinfo", false): nasty filename rejected
FS_OpenVirtualFile("data/maps/autogenerated/.mapinfo", false): nasty filename rejected
FS_OpenVirtualFile("maps/autogenerated/.mapinfo", false): nasty filename rejected
FS_OpenVirtualFile("data/maps/.ent", false): nasty filename rejected
FS_OpenVirtualFile("maps/.ent", false): nasty filename rejected
FS_OpenVirtualFile("data/maps/.bsp", false): nasty filename rejected
FS_OpenVirtualFile("maps/.bsp", false): nasty filename rejected
Maplist contains no usable maps!  Resetting it to default map list.

menu: unknown program name

This is a somewhat clean ~/.xonotic dir with a slightly modified example config.