centering rear end

Yes and no. Stock bearings will only work on stock axles. Green bearings will work on both factory and aftermarket axles. I'm not sure why stock bearings won't work on aftermarket axles but everywhere I see aftermarket axles listed they say "works with green bearings only"

It depends on the aftermarket axle. Dr. Diff's aftermarket axles work great with the factory tapered bearings.

As far as why it doesn't work, it probably has to do with the depth of the bearing surface on the aftermarket axles. And possibly the length of the axle itself.

I know I bought a rear end that had been cut down and new aftermarket housing ends put on it. It would only work with green bearings though, because the new housing ends weren't deep enough to allow the factory bearings to press all the way in. If the bearing surface on the aftermarket axles is made to match, it won't allow the tapered bearings to press on far enough.