Couldn't find an appropriate thread to link to.
You wouldn't be able to install them in rxMode, but you will be able to play them.
As mentioned above, a "legit" .cia is one created from a preinstalled game. They're signed with a generic signature so they can be added to your list of purchased games once you've created your NNID.
It also allows the preinstalled game to be merged with your existing NNID when performing a system transfer to a 3DS with a preinstalled game.
Once they're associated with your NNID they become yours, and can be (re)downloaded from the eShop any time you like.
Theoretically you could install all available legit games (there's about half a dozen I think) to a secondary 3DS, then perform a system transfer from your primary 3DS to it, at which point all the installed games would be acquired and linked to your primary's NNID.
One week later you system transfer back to your primary unit with 6 new games that as far as the 3DS is concerned are legally yours.