I am not at all surprised by your findings there is a big misconception due to the confusion of linear velocity and angular velocity.
The angular velocity is not changed. Average emf depends on the flux per pole (unchanged) turns ( unchanged) and frequency ( unchanged) . What has changed is the waveform of the output. With the sensible proportions the waveform is reasonably sinusoidal, when you mess the proportions it is far from it.
If you use a scope you may actually find the larger diameter gives a higher peak voltage ( but in many cases it won't), this affects the cut in speed a bit and you may benefit to some extent with Jerry connection. If you star connect the messy waveform violates all the conventional rules that we assume ( forgetting that they only apply to sine waves) and the result with star connection is miserable.
The assumptions of star giving 1.73 times phase volts line to line is based on sine waves. When you add in the differences between rms currents into the rectifier with different waveforms and the differing conduction pattern of 3 phase and Jerry connected rectifiers it all becomes confusing.
As you say you can still gain ( particularly with Jerry connection) if you use the available space to throw more copper at it but if you throw more magnets at it and increase the angular velocity as well then the gain is far greater.
For a given set of magnets and a given speed there is little to gain by straying from what has been found to work well. If you must go this strange route then don't use star. Delta is always problematic, so for strange things jerry's method seems to be the way to go.
Flux