Yeah most of the time the pinion depth will still be in spec but ANY brand pinion will do this not just FFRP.. the pinion bearings are usually what throws the pinion depth out of spec.. In fact the Ford special tool does not have us measure the pinion at all, we install the races in the housing and place the bearings in the races and thread this special tool in with a block on it facing the carrier.. in place of the carrier is a tube and we measure the distance from the block to the tube.. Notice they don't have us measure the pinion at all.
trust me I have set up a few of these things over the years..
My own car is set up the same way you did it becuase some ass stole the 8.8 stuff our of the pinion depth tool set.. I will buy my own soon but just the 8.8 stuff cost almost 300 bucks. the master kit to do all ford rearends is almost 1,000
Funny thing is many people wonder why dealers charge so much , one of the reasons is the hundreds of thousands of dollars worth of special tools we have that private shops don't.. sure we techs have our own tools but the shop has to have so much stuff it's not even funny.