1. The TID/SID of a Pokémon is that of its original trainer, who first obtained it.
2. You shouldn't have more than one unique encounter from a trainer.
3. It means exactly what it is labeled as; it is the trainer who has most recently handled the Pokémon. If it does not reside on the Original Trainer's save file, then it resides on the Latest Handler's save file (ignoring HOME basically not being a handler).
4. No. See #1.
5. Depends. Everything "depends". If it was able to visit Gen3/4 to participate in the Battle Tower/etc, then it should have sufficient level to have participated.
6. "Dangerous" no, "suspicious" yes. Do the mental math on how statistically possible it would be for you to have obtained it without cheating.
7. Having default/non-special memories is suspicious, because it's a sign they weren't really used in-game. If they have special ribbons and stuff that would have naturally obtained those ribbons, then you'd think you'd be more likely to have uncommon memories. Likewise the opposite; if everything has uncommon memories, that is suspicious too.
8. All auto legality mod does is generate things from the encounter database and update them to the battle template set you asked for. If you know how ALM's code works, you can see the patterns in how those are generated, and they're pretty obvious.
tl;dr - use bottle caps and learn how things actually work, else you'll produce obviously-generated 'mons.