this particular airframe lacked even the ability to align off a GPS Lat/long.
Still, even in a non GPS aircraft, the procedure is to enter the aerodrome ID, and align to the database ARP. It makes no difference to the navigation precision or performance of the IRS. And if you need to (ehm, ehm) modify, the technique is to slew the loaded values.
RAT: no gotchas. Just a sloppy SOP set, not aligned with error/failure modes asessment of the manufacturer and designers' intention.