The ones paid by the borrower end up in the APR calculations.
Be careful with that. The TIL is supposed to reflect the legal obligation between bank and borrower. Just because someone else may pay it, doesn't mean the borrower isn't legally liable for it. Unless the bank has an agreement with the other paying party, the fees should be included in APR calculation.
And that APR is the one that gets disclosed on the TIL and is the APR we use to test for HOEPA Sec. 32 and HPML Sec. 35.
Correct with the exception that you will have a different calculation for Section 32 loans if your loan is an ARM.