I don't have any once fired brass. I have some new lapua brass and some full length resized brass. I was trying to get the hang of my new hornady head space comparator and I noticed the new brass shoulder is actually shorter than the FL resized brass. Is that to be expected?

The FL resized brass rebounds to the chamber it was fired in so to speak.
Virgin brass is meant to fit in all chambers that SAAMI spec or even tighter

Either you don't have the sizing die turned down enough or the your pulling the case shoulder upward when you draw the expander ball back through the neck. New Lapua brass comes from the factory with too much neck tension. Polishing your expander ball will make it slicker. I spin polish mine using 600 grit wet/dry paper followed by 1500 grit wet/dry paper. It looks like a mirror when I'm done. This ease the passage though the neck. Be careful not to remove any more metal than necessary, just clean it up so it's shiny and you're done.

Some people use lube inside the case necks, I've never had to.