From what I've heard, yes, there will be a problem.  But it's fixed with a phone call.  Well, maybe.  It probably depends on who answers the phone.  It can be as easy as "hey IRS person, can you please move the payments made under SSN xxx to the MFJ tax return filed with spouse SSN xxx?"  YMMV.

I've also had problems with VA doing the same thing.  That was also fixed with a phone call.  No idea about PA.

I think this wasn't typically an IRS problem pre-COVID but when Congress started throwing money at people the IRS had to keep the EIP payments with the SSN because they didn't know what sort of return was going to be filed.  In doing so I think they lost the ability to automatically find spousal ES payments even though the spouse's SSN is on the joint return.  They may find it again in the future but I'm not holding my breath.  For now I would expect a problem.