If I recall correctly it couldn't read standard floppy disks either, but I might recall that wrong.
Microsoft did Apple a huge favor by making the Z80 Softcard for the Apple II.
I do not believe the concept of "commodity hardware" was well established when the Amiga was introduced in 1985, so faulting them for not using what eventually became commodity hardware is a little disingenuous.
I was using clones at the time I bought an Amiga, using commodity hardware, and nothing would interoperate with the Amiga.
I bought the Amiga intending to invest a lot of time and effort developing compilers for it. After I discovered its compatibility problems, I knew it would never succeed and was not going to invest in it. If DEC couldn't succeed with its pointlessly incompatible Rainbow, how could Amiga?
DEC did eventually fix the Rainbow, but by then its bad reputation was irretrievably lost. The DEC aficionados who had been holding out for a DEC PC had thrown in the towel and given up on DEC.
To me, that seems like more hardware compatibility than a Mac or II.
Like someone else said, the Macintosh was released at about the same time, was both IBM-incompatible and Apple II-incompatible, and it managed to succeed. The Amiga wasn't doomed because it did not use IBM-style keyboards or IBM-formatted disks or whatever.
Which reminds me that nobody knew that microchannel was not the way forward. Or at least nobody in the press. IBM had had already had hit and was still the dominate player. And there were M68000 based Mac's and Atari's along with legacy 8bit systems.
You are right on the other points though. Although proprietary hardware want the primary reason, it was one of the reasons of amiga eventual death.