I can't say I'm in the same boat as I have a TO box but I am all for this type of thing.
I think the boxes make up for the volume by extending the box back and up to the contours of the tank. This along with removing those big air filters (as you have done) account for much of the increased volume.
Without actually quantifying the lost volume due to the throttle bodies it's hard to determine if there is a difference in the volumes. However I do like the idea of a mod that people can do at home, especially if it gives us even a small bump in power. This can be a great intermediate, and pending testing, a potential replacement mod for those that can't/don't want to afford the aftermarket boxes.
2001 #62. Ohlins rear/valves, Micron high mount, HyperPro damper, SharkSkinz, Tyga billet triple clamp, Tyga Carbon Fiber fender and hugger, Ti bolt/custom subframe/alien motion 8 cell diet, 15/41 520, COP conv. PCIII, Venhill lines, modified air box, turn signals in headlights...<deep breath> ZG Touring windscreen, Tech G rear sets, CRF450 rear master w/HRC cover, Tokico 6 pots w/V-pads, CRG Bar end mirrors, PSR Shorty levers-use only clutch, wanna-be basic racer paint, Roman Gold PC wheels