Take this for what it is worth...
Lapua conducted multiple studies in the development and testing of their 6.5 CM brass and determined that the most consistent ignition and, therefore, consistent groups were found to be utilizing a small rifle primer (preferably small magnum) and an "undersized" flash hole.
Their choice to go with this relatively unconventional undersized flash hole has ruined many a decapping rod, to be sure. Redding specifically makes undersized decapping pins for exactly this reason.
Lapua dumped a good deal of time, effort and money into conducting these "best case/best potential" studies on 6.5 CM brass. It is for this reason that many other companies, such as Peterson and Starline have also introduced small rifle primer versions of this brass. In fact, many companies now offer both versions in several calibers for "discerning" shooters.
I'll be honest, I run a bunch of both the small and large primer versions in CM, from all of the above listed manufacturers and I have not found a significant difference at this point. It is entirely possible that I am not a shooter that is capable of squeezing that last little bit out to find an advantage in the small primer/x-small flash hole, but I guess it's nice to know that the potential is supposed to be out there for the taking.