Yeah, I agree, it can help improver their performance somewhat, but they have continued to perform well enough for me either way, so it has never been an issue.
When I first get my Eneloops, I'll do a slow discharge at 100mA on the C9000, then a break-in for 1900mAh for the AAs and 800mAh for the AAAs. This will help to refresh them somewhat out of the package and also tests their capacities to compare to later and helps me to arrange them in series cell sets which have similar capacities to use together.
So if they start seeming to under perform, I'll do another 100mA discharge followed by a break-in to help refresh them some more and to compare how they're holding up.
As I've mentioned in other threads, all my Eneloops are still performing like new, even my 4 year old first generation ones. They just keep on truckin'.