I'll interpret it as you meant Pixel OS when you said "stock Android".
The most painful one is likely the Play Protect API, which limits users of "non-certified" OSes, like GrapheneOS, from using certain apps, most commonly banking apps. It is not that common, but it happens.
Related to that is that Google Wallet doesn't work, due to the former.
Personally, I am lucky to not have any apps affected, but who knows when such a thing gets implemented...
Anyways, besides that, there's not much to add, except what @nologo said; an almost complete lack of Google services.
If you rely on other Google services (like for example Google Wallet), this'll be a major limitation for you.
Regarding the Pixel 10 Pro XL, I am pretty sure most of the hardware features should work OOTB.