Filing a joint 2023 tax return has no bearing on determining eligibility to make a 2022 Roth IRA contribution. If you file separately in 2022, the $10,000 MAGI limitation applies.
If you choose not to obtain returns of the excess Roth IRA contributions made for 2022 before the due date of your 2022 tax return, including extensions, you would owe the 6% excess contribution penalty for 2022. Resolving this excess contribution to avoid another 6% penalty on this same excess for 2023 would require either being able to apply the excess as a 2023 Roth IRA contribution (requiring that you qualify to make a 2023 Roth IRA contribution) or obtaining a regular distribution of an amount equal to the excess, with no adjustment for investment gain or loss, after the due date of your 2022 tax return, including extensions.
