On the version of vice x64 in Ubuntu 15.10, you can specify the config file to use at runtime:
x64 -config $HOME/.sdl-vicerc
I'm not sure why this isn't working in the desktop file. There's no error, x64 just fails to start.
Exec=x64 -config $HOME/.sdl-vicerc
Oh well. Looks like this might be more trouble than it's worth. Having a vice folder in apps and manually creating a link in the menu isn't so much work compared to setting up the tools and finding the vice source LOL. I might even prefer keeping my vice executable, roms, disks, config file and gamesave snapshots all in the one, writeable folder anyway.
btw, I really like how simple the filesystem layout is.