I'm curious about why you filed separately for those years. You could potentially correct the excess by filing amended returns with your spouse to change to married filing jointly. If that results in a refund for 2018, it won't be paid, but it would eliminate the Roth excess contribution. If amending to file jointly resulted in a refund for 2019-2021, that would be paid. It would also eliminate the Roth penalties. You could amend some years but not others, it's not all or nothing, although your Roth contributions would still be disallowed for any year you kept MFS.
Filing jointly usually results in less overall tax or a larger refund as many deductions and credits are disallowed or reduced when filing MFS, as you have discovered. (Rarely, MFS will lower your tax, so the only way to know for sure is to test both combinations.) Joint filing is always allowed even if one spouse doesn't work, as long as you agree. You can't amend from joint to separate after the April 15 deadline, but the IRS always allows you to amend from separate to joint, if you both agree.
It depends on why you filed MFS in the first place.
To change from 2 MFS returns to one MFJ return requires a little extra fiddling in Turbotax, we can explain further if you want to look into that.
