Honda extends the screen into the muffler for good reason, as it allows the screen to have far more open surface area, which equates to less restriction (assuming the screen is reasonably clean of course). The smaller flat screen, even though it has larger openings in the mesh (good), has larger wire diameter (bad) and less screen surface area (also bad). Without doing the math or setting up a test rig with manometer to measure the delta-P (pressure differential across the screen), my guess is the aftermarket screen probably has higher restriction.
The takeaway, is add screen cleaning to my maintenance interval.