Entering the Form 1099-R for a distribution from a SEP-IRA cannot be the cause of Schedule B being present in your tax return. The Schedule B is reporting something unrelated, probably from a Form 1099-INT or 1099-DIV.
As you pointed out, the purpose of breaking out the conversion is so that TurboTax can track the converted amount as conversion basis with respect to your Roth IRAs.
Form 5498 reports information to the IRS that you should already know based on your transaction history and account statements. There is no need to have Form 5498 in hand when preparing your tax return.
