Having approached IRS before you file a LMR return...

Here is one way to explain it -

Appearance cures all defects in jurisdiction.

It is very blatant once you receive refunds with the IRS blessing, after wrapping your mind around the remedy. Your boss will appreciate you keeping this between you and the IRS.

I believe you are transposing CtC (Cracking the Code) and other doctrine on remedy. In other words why go to the IRS and ask approval for something Congress has already approved?