The Quantum Time Locks and pruning of alternate Timelines are True, and have held true since they were established by the alien supercomputer on the moon three or four games ago. The Decline of Mystery is True and has held true since its introduction. etc, etc.
Honestly, the Decline of Mystery isn't really 'rules' in the sense we're debating imo. Like, it isn't a limit or anything like that, just a general trend/theme of the setting. And even it has exceptions. (Like, there's stuff that has more Mystery than other stuff that came before it, IE: Camelot , etc)
As for the Quantum Time Locks, well those aren't really understood very well atm, and stuff like the Servant Universe seems to indicate they're a lot less absolute than they sound. So yeah.
Basically, the argument is that the Nasuverse has no actual *hard* rules, despite everything about it's presentation trying desperately to convince the reader that it has.
There's a reason those omniscient types never say anything outright, it's because any definite statement would be disproven eventually lol.
Honestly the Nasuverse set the tone for this at the very start so it has nothing to blame but itself, just look at how FSN begins: the very first fight between Servants has an Archer (established as the class of bowman) engaging in meelee combat, then right afterwards, you have Lancer introducing the rules for how his NP works -- once the spear is thrust, the foe's heart has already been pierced / it always hits the heart -- then, he uses it against Saber... and it misses. So yeah, from the very start, any and all rules are only there to be broken.
Hell, if you think about it, the same thing aplies to Tsukihime too. I mean, the protag has the Mystic Eyes of Death Perception, something that causes death at a conceptual level, an absolute power that can kill ANYTHING, even imortals, inanimate objects, or abstract things like space and time... and the first time Shiki actually uses it on someone, the target survives, and doesn't even take permanent damage, not really.
You can argue all day every day about how justified those exceptions were and how the people who established those rules were unreliable narrators or whatever, but you can't argue that it sets a tone. And the rest of verse keeps going like that.