Yes, I think it’s relatively safe. I believe the current version has a system that allows you to basically save a “known good” set of preferences that you can restore if things go haywire.
I’ve used MacPilot for ages, and I prefer it compared to Cocktail, Onyx, and the others that do similar things.
It is possible to do something weird to your system? Yes.
But macOS has nothing like the Windows Registry, so even if something did go wacky, it probably would not effect much.