Very interesting post! I'm not going to quote it because it's so long...
I think TTL's "ST" would have more in common with the Miner-designed Amiga than the OTL ST, wouldn't it? Not sure the ST brand would be used, as that's rumored to be a subtle reference to "Sam Tramiel"... though of course it officially meant "16/32" in reference to the mentioned Motorola chips.
Probably, the Motorola brass probably would have greenlighted Miner's design where Warner didn't. Thus, Miner doesn't leave and probably works with Jobs on the project.
Doubt they'd go with the Mac all-in-one design, but I think the machine they produce, on-balance, would probably combine the best design aspects of both the Amiga and Mac.
As to the name...maybe Miner gets the honors of naming it and it ends up The Atari Amiga Personal Computer.
OTL, a projected 1850XLD was actually called Amiga, so, it just might happen.