You should not be using Pokemon obtained from cheats, glitches, or anything as a result of external modification in tournaments, as it is against the rules of both the tournament and our site.
Re-enabling unique encounters can be detected if said encounters leave traces in the save file (such as roamers), and if it originated from your save file and doesn't match that retained data/another "unique" same encounter is present, it is detectable. Official tournaments have disqualified players from having multiple unique encounters from the same save file.
Additionally, unique encounters can trigger other events, which can upset the logical flow of story progress/game state, resulting in unintended/impossible behavior and resulting encounters. There are examples, but it varies from encounter to encounter if it actually triggers unintended behavior.
Pokemon may be legal in isolation, but the secondary effects might not be apparent/overlooked until someone actually looks. Will they look, and what will they look for? Too general to answer.