It would not be hard to remove the transaction from RNI; all that needs to be done is mark SaveForInvoicing false and Invoiced as True; I’ve had to do this for a datafix. This should easily be done with a BPM at the time of receipt.
As far as getting the GLs set, then if I set an AP Account GL Control on the specific suppliers, create the new control and set the clearing account to be the “intercompany” GL, then all should be well, right?