Because the pump chamber is so small, you "may" have to remove and run it without the suction screen to get it to fit. Ive also seen where people will shave the front of a pump slightly to gain just a few more millimeters to get the pump to fit.
I love the all-glass construction of the waterbox, but it does make it tough to modify. I wish the back chamber was just a 1/2in larger in all directions - it would open it up to many more pump options.
The single 1/4in is a great option - especially with the nano - because it slightly over drives the 1/4in RFG and produces a surprising amount of movement throughout the tank. in fact that's how we run the Waterbox 10 cube in the front lobby of our office
This is the Waterbox 10 we maintain here at the office. All flow in the tank is created with a single 1/4in RFG and a SICCE nano. It been up and ruining for just ab out a year
Don't mind the Aphasia - it s mixed reef with Nems tank

LOL
This is what he 1/4in Waterbox Flow Kit looks like installed with the single 1/4in RFG
Waterbox Flow Kits
vividcreativeaquatics.com