If there was a lump sum general seller credit to offset various fees adding up to that amount and not a specific charge being paid by the seller, it would be in the tolerance test, correct?
Yes. The comparison for testing for tolerance violations will be between the cost estimates you have made via loan estimates and the actual costs paid by or assessed on the consumer. If your closing disclosure shows that the consumer paid $500 for the discount point, but received a seller credit of $750 total that "reimbursed" the consumer for the discount point and for a $250 radon-abatement service, and the discount point wasn't previously disclosed as a cost to the consumer, there will be a $500 tolerance cure (all other things being equal).
Caution here: The finance charges and APR on the loan must reflect the contractual obligation between the consumer and the lender. My understanding here is that the discount points will typically be a borrower obligation, and would be included as a PPFC, and thus be reflected in the APR. Only if there is a legal commitment to the lender on the part of the seller to pay the discount points would they be excluded from the finance charge. Your LOS may not be able to handle the discount points correctly if they are carried in the seller-paid column of the closing disclosure.