Just spit balling here, but, . . .
But one of the factors that can affect WC readings in a flue pipe is not just pressure difference,but exhaust gas speeds too. You can see examples of this variation in readings by plumbing vacuum gauges in at different sized areas (carb venturi, intake manifold runners, intake manifold plenum, etc. ) of an automotive intake system.
Another thing that may be happening that also limits how much the secondary's "pull" air is if at higher WC , the fire is burning hotter (as measured downstream in the flue pipe, not the firebox) , therefore producing more exhaust gases and even though to you see the WC reading increasing at the flue pipe, that WC may "appear" to be higher, because of the higher exhaust gas speeds from the increased heat output of the firebox. Meanwhile, back in the firebox where you can't get a WC reading, the increased exhaust gas "volume" in the firebox is now actually at a lower WC, so that the secondarys see less pressure difference ???
As it burns hotter it backs up in the firebox because it acts as a plenum, dropping the WC at that point as the gases have to speed up to exit.
One thing I've noticed about the box stoves is they can pull alot of WC on a mano gauge.
I think that, unlike our old stoves, that have such a smaller firepot in comparison to their 5 inch and 6 inch flue pipe size, your big box stoves are closer to the maximum firebox output for their flue sizes. Being that close in firebox to pipe size will give much different exhaust gas speeds, which you can only see as increase in mano readings, but not velocity.
Being that much closer to max firebox to flue ratio has to have an affect of how (and when) your secondarys draw.
Or not, ....