Everything you install, thats not using an official game/title id will get added to your play history and be an instand flag for nintendo when the history gets send to them. Its also one of the reasons nsp forwarders arent supported officially by Atmosphere, since they just aren't safe to use.
Modding a real game on the other side will only be a problem if you play online with it, or install it from an nsp/xci.