Honestly, I agree, the "hey, your save is edited" warning is too... otrusive? imo, especially when in TiTS there's none of that
I do want to cheat or edit my save to try out things, especially when some things are just too annoying, like the 32 Kiyoko kids to bring her to her last transformation, it takes at least 96 Sleep actions, it's a lot for only one character
Why not just put a little logo somewhere, or as someone else said, just put a warning on the option menu (or codex, or anywhere else really), but not a pop-up each time you load