I'm a little confused by that you are saying,
You can either have a centered pinion or equal length axles, not both. If the pinion (drive shaft) is centered then you will have axles that are about 4 inches different in length (depends on the center traction device).
Either way,
There will not be a problem with either of those setups, typically you will never feel a difference from having centered pinion or equal length axles.
Jason
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