I see this as a false dichotomy. You want this to be only a credit or an itemized deduction under claim of right, but those are not the only options. If the payments to the school for the excess SE had happened in each year, the self-employment would have been reduced by the expense to the school. That doesn't make it a claw back. As for it being historic years, a cash basis tax payer incurs that cost when it is paid. That means it is not under the claim of right credit or itemized deduction. You did not really ask whether or not SE Tax was in the computation, but how it is included, because you didn't find it stated in the text of the section you want to reference. Yet, the IRM instructions points out it goes to the original income forum, so on Sched C means it will affect SE by reference.

"If you do not have anything to add about whether 1341(a)(5)(B) refers to SE tax, based on the language as finalized, I'll wrap this up and thank you."

You presented a pretty specific scenario with what appears to be different parts. The question you present for 1341 seems to be first to determine whether it applies to all, some, or none of your scenario. Unless this was only for discussion's sake. You can see how this Q&A has resulted in revealing details that matter, as we went along. I hope that was useful. Sorry no one has given you a definitive enough answer.