Two Sets of Rules, the Good and Bad?

[noob]

The issue arise when using some abilities that then feels constrained by the arbitrary barrier between the two sets of rules.
For example you say that sir Kay the CR5 knight that the team fought at the end of their first campaign due to a misunderstanding and a lost letter could shrug off many abilities through his extreme training (legendary resistance or something) and sir kay was exceptionally good at fighting (CR5 boss monster and not just an ordinary CR5 monster)
Now much later the adventurers gets access to true polymorph and for some reason one player with a fifth level fighter that is otherwise similar to sir kay joins the table.
That fighter could be true polymorphed in sir kay which is stronger than him but that is not the only weird thing: you could also turn a rock in a sir kay but you can not turn sir kay nor a rock to that adventurer despite that adventurer seemingly being weaker than sir kay and sir kay being very widely within the limits of what you could get by transforming a rock.
Furthermore it also means an adventurer can have legendary resistance but only while transformed but they can not get legendary resistance by training despite sir kay being an human and having gained legendary saves somehow.
So now the wizard having read that true polymorph can not turn a creature in a creature stronger than itself is definitively confused by that situation(the wizard player can just read the rules and figure out it is due to the pc/npc separation)

The problem comes from abilities that handles in a fundamentally different way npcs and pcs while both from their own pov are living in the same world and are of the same species.
Why such abilities even exists?
Could dnd finally make polymorph make sense one day?