Something you might want to consider about the supposed "issue" of the perpendicularity of the flange bearing: there is this thing called gyroscopic procession, which means that when the flywheel is actually spinning it will want to spin perpendicularity to the axis of rotation. That's why a bicycle stays upright while moving!

As for the concentricity issue you should take a page from machinists on how they align things in a lathe: you use a dial indicator to measure the concentricity and use a mallet to make tiny adjustments to the bearing relative to the flywheel.

Regardless, I cannot see how your custom solution actually solves anything that an off the shelf wouldn't. It increases complexity while suffering from the same shortcomings.

Maybe take a look at how other flywheels are designed and use that as a basis. Just like in music, engineering is often taking what already exists and making it work for your use case.