I don't think this limitation will be overcome one day. The 3DS has to reboot into GBA/DSi mode to launch these games, so emunand is not usable.
Anyway, install them on both, and keep your emunand. It works that way.
my stuff is on eshop, so i will have to use my tools to dump a cia, haha
it would be great if luma would support installing of personal legit cias.
@Aurora Wright - do you have any idea on why cias that have a console id in the ticket do not install?
but as soon as we edit (and break the signatures) of the ticket's console id to 00000000, it installs?
because of this problem, we cannot install 'personal legit' cias, that FunkyCIA creates.
is there some check happening in the fw that doesn't allow cias with that contain a console id?
any information is welcome

thanks