I'm going to go out on a limb a bit here and suggest the larger chamber and smaller piston dish would be a preferable choice.
My rationale would center on shrouding of the valves: Smaller chambers may move the chamber walls very close to the valve seats and may serve to limit flow, something with which the small-bore modular already has a problem.
I actually don't know what the chambers between your 2 choices look like... but maximize the quench area. The quench is the area where the piston nearly kiss the face of the head at TDC. A larger and tighter quench area will make more power by making your engine less knock sensitive. When the piston approaches the head, all that volume of air between the head and the piston gets squeezed out and creates a lot of turbulence. This turbulence increases the speed of the burn, which makes a significant difference in the knock characteristics (much less likely to knock).