I could go either way, since a L5-22 run is not the way I personally use this program, but it would make more sense to start with the 95,200 as part of the score.
I can imagine that some might want to practice playing through full runs (minus start) at "x" pace, and I think it would be more helpful for them to have a "real" score to look at throughout the game, rather than one that's off by 95K. (Ie, "at the halfway point in Level 12, my score should be this.")
It's a little strange and potentially confusing for the program to report your pace as "x", but for the actual score on L22 to end up at "x-95K". If you're figuring un-earned points into the pace, you should probably figure them into the actual score too.