I'm not sure the question still is clear.

You don't get a refund of SS from the 1040 filing. If there is too much SS withheld on the W2, the employer would need to refund that.

If I understand you right, the W2 and the SE will result in a total SS but a max that has been reached, so you don't pay as much, which is really against a Balance Owed, as long as the amount withheld on the W2 is at least what was owed. In other words, the SE would be considered if it results in more owed or not; not the W2.  If combined there is not as much owed as the W2 shows, that would not make any sense at all.

And this is just SS. SE is SS + Medicare. That is where your Excel might be helpful.

And if this simply is an amended return issue, then all amounts paid are considered against amounts owed. The 1040 is the collection medium for SS, in the case of the SE, of course. So, a 1040X might reflect that too much was paid in for "taxes" and the amended filing will reflect corrected SE info. Is that what you are asking about?