The top wing is often at a higher angle of incidence than the bottom one. That is one thing to investigate when trying to figure out what he's talking about. It means the top/front wing usually stalls first, and the lift remaining from the lower/aft wing will help lower the nose to aid stall recovery.
There are a ton of other issues as you say... Each wing has a different moment on the center of lift so each wing contributes differently to induced drag and drag from tail surfaces, even if the wings had the same angle of incidence.
Wing-fuselage interference drag and as you said, pressures between the wings and wingtip vortice effects, will change things too.
If you have time, see if you can look up why the beech staggerwing had the wings staggered backwards from most other biplanes.