The priming system works great on a 550, there is no need to hand prime.
If you did hand prime, you are throwing away the advantage of a progressive (Speed).
You can "feel" the primer seating, and the bottom of the primer pocket, if your primer pockets and brass are prepped correctly.
The thing that will screw up the priming system is spilled powder, and that is the fault of the loader.
Just take apart and clean, good as new.
If you want to load in volume, batches of 500 or 1k, buy extra primer tubes and make a primer tube holder.