I'm not sure though about the magnitude of the effects. I never noticed speaker break in on any speaker I've owned, (and I'm a careful listener) so I just have to infer what I can from outside information.
I mean, my system can still "sound" different at different times to me, and my speakers are far past any break in period, being years old. So I bet, in my case, it's more down the changes in my mood, state of mind etc and how it affects my perception, than to the system (as our minds and perception are vastly more plastic than the likely changes in a system day to day).
I don't claim answers; I'm trying to figure my way through high end audio like anyone else.