Some of the tunes like the JB3 when it first came out set off tuner faults that the dealers can detect, but most tunes now have looped around that. Only BMW Tech Support (PUMA) can detect if you have a flash tune, increased rev limit, etc., but that only happens when you have a serious issue with the engine/transmission and they are called in for help/authorization for expensive part replacements. As for maintenance services you will not need to worry about have a tune, they have no reason to hunt for it.
As said above, most tunes now have reversible flashes. VF Engineering just released their NA tune for the E9X M3 that has reversible flash and fault code reader.