Is the group handle 'tighter' in the group? If not, puck compression due to differences in distance to the shower screen can probably be discounted.
I think it highly unlikely that there would be a significant difference hydraulic resistance between the naked and the original, due to geometric differences in the flow paths, unless the bottom of the basket was very close to the portafilter.
There is some who seem to think otherwise, however my thoughts are that subtle variations in the way the handle influences how you dose and tamp are likely at play.
Might even be possible that the naked doesn't heat the basket/grinds as much whilst filling and tamping, altering the temperature of the water once the pour starts, altering the rate of extraction and thus initial viscosity (thus the hydraulic resistance of the puck and ultimately the flowrate ).
My second crack.