1) don't file an incorrect return; don't file a return that shows a contribution penalty when you did not make a contribution.
2) form 5498 is not going to correct at the IRS errors on your filed return.
3) "IF check the box in Turbo Tax that the amount was converted to a Roth IRA, an excess contribution to my Roth IRA results plus a 6% penalty."
I don't see how this can happen. I'm looking at TurboTax 2018 and it does not happen when I tried your scenario just to be sure.
What is the amount of the "Excess contribution"?
Maybe you have an unresolved excess contribution from a previous year.
