Were the frame axle bumpers different for Dana's on '69 Plymouth b-bodies ?

Yes. The hemi and 440 with 4 speeds took a beefier one. Most likely due to the dana. They all fit ok either way.

I don't see the logic ... how often would the rear end bottom out ?!?!

As often as the idiot driving it made it do it
I've made the mistake, more than once , of riding with someone I didn't know very well that changed how they drove when out drinking, several bad experiences

Yeah well, those days are gone. I'm older and wiser and being more cautious with the years I have left!

The A12 cars had the std bumpers on them even though they had a Dana. They were 383 cars taken off the line so they were missed.

They were built off 383 spec cars, they never had the hemi reinforcements , only the hemi rear springs and tbars ... just like axle package 383 cars, the pilot cars may have been taken off the line but once actual production started they were built in batches on the line with only special treatment for the hood install once it was fully assembled.

8.75 and dana 60's had the same axle tube diameter ????

Your correct: up: 3.0 O.D.
Dana 60 came with many different axle tube sizes in them depending on the application. I've own them with 2.5., 3.0, 3.250 and 3.500 O.D, axle tubes