The reason for the flip is you can keep the retainer in the OEM position on the axle and get the seal lip riding near center on the polished shoulder of the retainer. The updated seals from Toyota were an improvement due to how pliable they are but it caused an issue that the Toyota engineers didn't think about or maybe didn't care. The seal lip of the new seals now sits 2mm more inboard than the old seal. With the OEM orientation of the inner retainer, bevel facing the seal, you first have to push past the 2mm bevel to get up onto the shoulder. By flipping it, you gain the 2mm back from the seal re-design because the seal immediately gets up onto the shoulder with the retainer flipped, bevel facing the ABS tone ring.
If you kept the inner retainer in the OEM orientation and with 5mm of polished axle showing above, the seal will be riding very close to the bevel which isn't good. With a little axle play from the bearing wearing over time, that seal will ultimately ride on the bevel and the seal will fail.
They say a picture speaks a 1000 words. The seal witness mark in the center is where the original seal from the factory was riding. The seal witness mark near the bevel is where the newly designed seal rides on the retainer if you don't reposition or flip it. I pulled this retainer off one of the axles I worked on. It's obvious somebody thought they could just replace the seal not knowing Toyota redesigned it.
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