Good research with definitive measurements!
I've struggled many times with rear axle seal leaks. I think it's one of the most annoying faults by Toyota concerning 3rd gen 4Runners. Usually it was after every 30K miles or so when mine leaked, so they would seem to typically fail due to wear. But one of the most recent times was when I took the axles to a 4x4 shop that supposed had lots of Toyota experience. I just wanted to replace the bearings. They smacked everything together tight without leaving the gap that's specified in the FSM. I didn't realize that until it was too late. It leaked almost right away. Maybe older years of Toyotas didn't need a gap, so the mechanics that think they know what they're doing just smack it all together. Maybe it's because older Toys didn't have ABS, which probably started in '96 anyway.
I was very surprised by the picture you posted about the difference of the inside of the axle tube on a non-ABS axle.
The very first time that my axle seals leaked, it was repaired at a Toyota dealership. They actually didn't press the retainer ring on quite far enough, which led to it rubbing against the raised section inside the axle tube. I didn't notice drag or noise, so it was like that for a long time. It actually didn't lead to a leak either, but left an obvious wear mark on the metal inside the axle tube. I was lucky that didn't cause other problems.
One observation of mine was that different brands of axle seals have a surprisingly large variation of several dimensions of the rubber seal including the inner diameter. I bought a few from different shops and from Toyota. Sorry I don't have details to post now, although I could look for my notes. I was just shocked that one or two seemed to be too large and would barely touch the retainer ring anyway. Others might be a decent inner diameter that would seem tight, but the extension of the rubber to the side might cause it to extend beyond the edge of the retainer ring. For example one extended to the side beyond the outer metal, while another one remained completely within it.
This was such a frustrating topic to me that a couple years ago I gave up and invested in the Front Range Off-Road Fab full floater kit with Supra disc brakes. It was a very expensive solution (about $2000), but it completely changes the method of sealing the axle (now at the end of the axle), I now have a reliable e-brake, I got rid of the drum brakes (woohoo!), and I never have to worry about one of the rear bearings failing to cause one of my rear wheels to leave and pass me on the road (which really was a concern due to the frequent leaks and the poor design that Toyota mechanics couldn't even get right). I have had no problems with the axle leaking any fluid since the upgrade, although it required a little creativity to get the e-brake cable slightly re-routed and tight with a short extension. I did lose ABS ONLY because there's no longer something that's the right diameter to slide the ABS tone ring onto the axle. But it would definitely still fit in there if I get the time to design a piece of plastic to hold it. I still have the ABS sensors in place.
