The thing is that I used a 357A with my old (now sold) 1200 1d4 with no problems thatsoever. looks like I never should have sold it
For some reason I was under the impression you were testing an FZ-357A! Probably because that's what could fit in an A1200 (I have one in mine).
Just re-read your 1st post and saw it's the bulky FB-357A (so I guess you're having your A1200 permanently opened up

)
I have an FB-357A as well, in my A500. It also works without any problems.
I also have a second FB-357A which I bought as non-working. At first it worked fine but only as a DD drive, then a couple of days later it decided it was an HD drive too and worked correctly in HD mode as well. Didn't give it much thought as it's never failed since.
But I've never tried either drive on the A1200.
I could see HD-ID detection problems happening on those weird Escom A1200 boards which have the RDY line disconnected from the internal connector, but those are rev 1D.4 ones and IIRC you're using a rev 1B board.
When you say softkick are you referring to something like relokick but with a 2.04 image instead of a 1.3?
I had stuff like skick and zkick in mind, but sure that too - if it isn't made specifically to downgrade to 1.3.
I'm not much into software so I have no idea if that approach would even work but it seems easier than individually patching trackdisk.