Ok, to you all, lets put up everything together and do some thinking.
1. Clearing time is important. Finishing a stage too fast, gives a red flag to devs.
2. Taking no damage at all. If you use god mode or dumb enemy, use it ONLY after your squad get some damage first. If you get Scarlet, it will too obvious if she doesn't take damage in a stage because her skill is sacrificing some of her hp for some damage.
3. Power level requirement. If your squad needs about 100 power to recommended power level, try using without mod first. If you have bad rng or bad run, try using mod. Even with enough power level, in different scenarios (e.g. defense stage or boss stage), you still can fail because some enemy have unique attacks (like stun, heal, extra damage etc). .
4. Bond level, equipment and cubes also important to your squad's power level. I think base upgrading also affect how the devs determine how legit your account is. This also linked to how long you've started playing the game. Imagine a 2 old days account have cleared 16 chapter, its obviously raised a red flag.
In conclusion, IMHO, only use mod if you fail a stage or needs more time for clearing a stage after you maximize everything a F2P would do.