What??? How do you suppose mixture has any effect on manifold pressure? It doesn't. Mixture has an effect on power, and temperature, but not on manifold pressure, unless it changes RPM. For a given RPM, mixture has no effect on manifold pressure.
Manifold pressure is a function of throttle position and engine RPM, period. For a given engine RPM, increasing throttle will increase manifold pressure by reducing the obstruction to engine suction through the induction. For a given throttle plate position setting, increasing RPM decrease manifold pressure.
In normal operation, increasing throttle plate position increases manifold pressure in much the same way that removing an obstruction from a vacum cleaner hose increases the pressure in the hose...by removing the obstrution to the hose. Your engine is an air pump, and consequently a suction machine. The induction represents the vacum cleaner hose, or suction end, and the exhaust represents, well...the exhaust. Put your hand over a vacum cleaner hose, pressure drops in the hose, just lke closing the throttle on an engine.
For two otherwise identical engines to have differing manifold pressure for a given throttle setting with identical RPM, you either have an induction leak or an indication error. This assumes the same engine RPM.
Take the theoretical shopvac, turn it on, put your hand over the hose. Measure the pressure in the hose. There's your manifold pressure; the hose is the induction manifold. Cut a hole in the hose. Hose pressure will rise, and there's your induction leak.
If it's an indication problem, you may see a higher manifold pressure, but you're also going to see temperature differences if you have a means of monitoring them. The same is true of an induction leak.
How matched are the engines at idle?