Interesting. And uni, you were just telling me yesterday about a common failure you've seen being "the OS keeps saying the disk is not initialized… when there is no disk even in the floppy drive."
I was thinking about this more, and I believe it means the RD line on the floppy connector is somehow stuck at GND. I'm pretty sure that would lead to the behavior you're seeing - complaints that a phantom disk is not initialized. That's pin 18 on the external DB-19 floppy port (see http://old.pinouts.ru/Storage/MacExtDrive_pinout.shtml).You can test this theory yourself by checking pin 18 vs pin 1 with a multimeter. With no floppy drives connected, RD should be 5 volts because there's a pull-up resistor on the logic board. If it's anything substantially lower, or 0 volts, then that's the problem.
If this is due to some kind of logic board failure, then the "disk is not initialized" errors should persist even if there are no floppy drives connected to the Mac. That's something you can test.
If it's a failure with the drive itself, then I would expect you'd see 5 V with no drives connected, but a constant 0 volts with the drive connected (measure the voltage at the internal floppy port if the drive is connected externally, and vice-versa).
Since you swapped drives and it didn't fix anything, I'm guessing it's a logic board issue. Could be a faulty SWIM, bad Bourns filter (does the portable have these?), a fried pull-up resistor, or a broken trace on the logic board.