So the FA regulation you posted is of no consequence and your original point that the club loaning the player wouldn't have their wages reflected in their total is surely wrong? As the FL calculation removes the wages of the loan player from the total wage bill of the loaning club for the purposes of the FFP calculation.
You really are missing the point
When FL clubs and the league management calculate FFP allowances are made in respect of sums paid out and received in respect of players on loan. That has nothing to do with who pays the player.
Think it through. Everton didn't pay all of Gareth Barrys wages when he was on loan. If by going on loan he became an Everton employee hwo and who paid the balance of his wages?