I'm A Banana
Potassium-Rich
No worries on that score. If you set a precedent of "magical effects cannot cross the Polymorph boundary" there are plenty of other gamebreaking combos you can create. Rakshasa claws? Ha! Now I'm a giant ape wielding my giant magic sword.
Unfortunately, that would require hands...so that's a no-go according to a strict reading of the spell ("it can't speak, cast spells, or take any other action that requires hands or speech")
When the Rakshasa curses me, it's the ape who is cursed, not the real me. Barbarian dominated by an Aboleth? Instead of Dispelling, just Polymorph instead--it has a better action economy cost. Vorpal sword? Who cares if I'm a limbless crippled giant ape now, it's only temporary. It's not just free temp HP any more, it's a free character. What happens when a Magic Jarred character gets Polymorphed? Does the original soul pop back into the body somehow, or is Magic Jar an exception?
I am pretty OK with most of those "defensive" uses of the spell. I don't have much of a problem with it being used as a high-cost "get out of a status effect free" card, especially because even as a T-rex, your barbarian is probably taking a bit of a nerf with the spell (and with the low mental ability scores, shouldn't be a problem to re-dominate!

As for Magic Jar - you wouldn't be able to cast it while polymorphed, and since a creature under the effects of polymorph is a beast, you wouldn't be able to use it on someone who had been polymorphed either ("you can attempt to possess any humanoid..."). If you tried to possess someone under the effects of something that can do humanoid, like shapechange, I'd might say that you possess the form that has been shapechanged into. Like, there's some old decrepit wizard who has shapechanged into a comely elfin lass and you use magic jar and then try to possess the comely elven lass (you pervert) and you find yourself possessing a comely elven lass...and are perhaps surprised to find that this is an enchantment you're concentrating on. Since you'd be hitting the natural CHA save of a caster high enough level to cast shapechange, you may now be justifiably concerned about repercussions for stealing the comely elven lass body of an 18th-level spellcaster.

I'm not complaining about this (nothing that happens on the Internet affects my table) but I am pointing out some things that I'm considering as I make my own ruling/theory of Polymorph. There are complexities and broken combos either way.
I think making the barrier a hard one does away with the worst. Using it to wiggle out of an ongoing condition for an hour using your Concentration slot would be a neat trick, but typically less effective than just removing the condition or getting a save or making the condition-inflicter eat a Concentration roll or six, so I don't have many problems with that niche use. But at least you can't stack much on top of the critter you turn someone into to escalate it too high, and you'd have to use your actions in the moment to do it (limiting the "buff before you fight" abuses). It's a high-level spell, so I'm comfortable having it be pretty potent.