You certainly can use trim in any manner you like. This procedure is simply to dial in a no wind AL trim setting. If you later adjust trim, for what ever reason, if you do not move them back, the HFP will read the new positions as center the next time you power cycle and it will fly fine. In AL mode, it may drift as before.
Over on RCGroups, you'll find photos of a fellow who didn't disarm his multi. He approached it and kneeled down to do something and somehow, the receiver/transmitter signal was blocked. The multi went into fail safe mode and the motors spooled up and it jumped in his face. 68 stitches later and a lesson learned that could have killed him. Go and look.. I think his name was AV8Chuck. Not sure though...