It seems the old Mossie did gain TAS faster at increasing altitudes than the new one. It also looks like that the new model's supercharger's first stage has a higher FTH than the old ones.
I'll need to do more tests, but my charts in books put the Merlin 25's FTH at 13,000ft, which is why I tested it there. Got higher speeds even though boost wasn't hitting +18lbs once I got over 12,000ft. Boost in the old Mossie was almost entirely disassociated from actual performance, so I ignore it.
Also note that the new Mossie's MIL starts out the same, well, 1mph slower, and ends up slightly faster. The dip at 5,000ft is a dip.