I would like to know the basis of this statement. As stated earlier, the reason that (at least some) non-A9M0106 800k drives don't work without the HD-20 init is the TACH/divide-by-zero ROM problem which is completely unrelated to "how an eject happens". I just set up my 512k to make *sure* my memory wasn't faulty and I can confirm that an attached A9M0106 behaves identically to an internal drive. IE, I can boot from it, I can remove it and swap in a different disk using the "Eject" item on the "File" menu (I did mis-remember that you could also drag it to the trash, that's what triggers the "you can't throw the system disk away" message), and it auto-ejects the floppy before rebooting when you request a shutdown. I ran the whole drill on both the internal and external drives and the behavior was 100% identical. For the tests I used two different System 2.0/Finder 4.1 floppies (with "MacPaint" and "MacWrite" on them) and the HD-20 init was definitely *not* loaded.
When you tried your System 2.0 floppies on your Plus' *internal* drive did it also refuse to eject them during shutdown? To be clear, when you ran these tests with the external drives on your Plus were the drives directly attached to the Plus, or were they chained off the HD-20? I don't know why the latter might make a difference but just trying to kill some variables.
I'm going to throw a genuinely stupid idea out there: *if* the eject-before-shutdown doesn't work on the Plus' internal drive either I'm going to have to say I wonder if there might be some sort of virus on these boot floppies that's messing with the system. Viruses were actually a depressingly common problem in the Mac's early days.
