Quiet large part of, for example AntiVir's HEUR detections is based on how is program protected, so going in similar direction is a smart thing imo (especially if it's done in a smart way).
HEUR/Crypted were quiet common and as far as i can tell it all depends on how many layers and what kind of cryptors/protectors/packers are used together. The more exotic combination, the higher chance of getting flagged. Regular programs are usually not using anything similar or in a very very rare cases.