What about MiSTress 1200? (also what compatibility issues MiSTer FPGA core have?)
https://www.8bits4ever.net/product-page/mistress-1200
That will make it very expensive. It would be much cheaper, for example to partner with Heber ( https://shop.heber.co.uk/shop-all/mister-multisystem/ ) and ask them to design a MiSTEr based motherboard in a shape that would fit the A1200, with all the extra Amiga related ports of course (such as RGB15khz, joystick/mouse connector, external drive, etc.).
Regarding incompatibility, I don't know the exact details except that it is not very accurate. I believe there are issues with the Turrican remake (the one with the PC VGA garphics), also when I play Shadow Dancer on MiSTer using Amiga Vision, in A1200, when the main character sprite jumps it glitches.
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