I've not actually played and have rather seen other people play. My issue is the way your anti-cheat works-- theoretically, it is 100% possible to trigger it through normal gameplay, looking at the little code that I can find and drawing conclusions based on helping the streamer I mentioned experiment. Not only that, but it's also easy as hell to bypass if you know how it works.
Adding a "you beat the game now you can cheat" option would be cool but not solve the issue.
I don't think it's entirely the grinding either. Your anti-cheat doesn't trigger on money; experience and levels are easy to manipulate. From what I've seen a significant facet of the issue is your boss fights and a few relatively overpowered random foes (a trainer with a Pelistorm, a youngster that just randomly has Mega Evolution). The mutated-fused-whatever Pokemon are too powerful and Modified Electivire is... kind of ridiculous, all things considered. I get that you wanted the battle to be difficult, but (in specifically R's case) making it literally more than six times more powerful than Arceus is not a good solution. "Excessive" is not a good trait to be given.
As for the "importance and weight" aspect, that 100% depends on the player. Oftentimes players cheat because they feel the game is unfair, and I think Empyrean is one of these cases.