Years past I burned a lot of IMR4831 in a 300 Win Mag;velocitie un that particular barrel were in the 3125-3140 range with a 180 gr Nosler Partition.
But the rifle had been "long throated",meaning bullets could be seated out to a longer OAL. Charges were heavier than the manuals show; how much is not really important. The load was fine with my components in my barrel.
What you are seeing is not that unusual...many manual loads will do in the 2900 fps range with 180 gr bullets from 300 win mags and 24" tubes ,and will vary from what the manuals say you should get, due to test barrels being held to tighter tolerances as opposed to your factory barrel.
Different throats alone can show 100 fps difference. Not to mention the differences in lots of components between what you are using and the manual components.
And yes brass can have different internal dimensions resulting in some of it holding more powder than others.
Add all this stuff up,and you end up with velocity variations between what the manuals say and what you are getting.The manual people are not lying to us;we are simply using different components and different rifles.
In your case, I would say the manuals did what they are supposed to.....give you a trouble free load that works in your 300 Win Mag(and likely thousands of others)without risk of blowing yourself up;yet delivers a decent velocity level at safe pressures.
These differences are intellectually stimulating sometimes and make for great conversation but I suggest anyone not dwell on them too long;concentrate on what your rifle does, and just go shoot it.