Well there is not actualy a real person sitting behind the computer at all times watching and trying to catch somebody cheating, flagging comes into place, for example:
1- "You use 1 Wavewin mod on TM or event without using the "waiting 90 seconds" or whatever it is method and you get instant point locked and flagged.
2-"You use 1 Wavewinmod on TM or event while you do use the "waiting 90 seconds" and you don't get point locked because some "ingame timer" but you do get flagged (for finishing within 1 round?)
The game doesn't send or receive data from the server besides when you start a battle and when it finishes. Obviously the game recognises when you 1 WaveWin instantly within a few seconds and finish the match since this is where most people get point locked on TM and eventually get banned proving the game registers at least the amount of time spent in a fight from start to end, BEFORE COMPLETING the fight, example 1 proves this.
So I'm guessing, if the game can store the time WHILE PLAYING and send the information containing the time spent in a fight to the server AFTER a fight, then the game probably can also register how many battles you actually fought WHILE PLAYING and also send that information to the server AFTER a fight. Which will probably flag some registries on the servers part, and these flags may not be directly related to a point lock, which is a direct-computer automated measure from bandai's side.
So in example 2, you won't immediatly get point locked because you bypass this "timer" and also the point lock since they are related so far that we know of directly. But the game still knows you finished in 1 battle and you probably will get flagged for that and eventually banned. When you get flagged this way in events EVENTUALLY an actual person will have to take a look at this BIG RED !!! in the screen and actually review your account data, and come the conclusion that you are cheating and boom, ban hammer.
Maybe Infinite Box space is also server recognisable, maybe not, I don't know, these are just what I think based on the best of my (techno)logical knowledge and I don't think its impossible.
At any rate, use at own risk at all times