"Do we have to keep track of the basis from old employer 401ks that are converted to Roths?"

Every specific matters. For instance, Employer 401(k) to Roth typically is the split of the Post-tax and Pre-tax amounts. Upon termination or retirement, post-tax amounts qualify to go to Roth and untaxed earnings and pre-tax amounts go to Trad IRA, when an employee "takes their retirement funds" with them. Keep in mind that Roth 401(k) has an RMD requirement that Roth IRA does not. Also, there are the 5-year rules considerations for Roth. So, yes, you track the Roth basis, even if it is never deductible and even if it is not being reported, because you don't know what might happen in the next year or two for that taxpayer's life.

"Or, do we simply need to report the amount that is taxable in box 2A of the 1099R?"

You enter the 1099-R as it is reported for the taxpayer, and you enter the rest of the tax prep info as you know applies. The 1099-R code might show "no exception applies" when one does apply, but the issuer isn't aware of the exception. The issuer is not tracking basis, either. The taxpayer reports what applies.

Just recently on this forum, someone has a SEPP distribution, which I have seen the 1099-R issued as code 1, which was not in error but Uninformed. The issuer isn't responsible for the establishment of the SEPP. The taxpayer is responsible.