Take a good look at the card again.. the CPU is pointing inwards to the computer... there should be no problem putting on the trapdoor with the card inserted from a formfaktor point of view... though I would at least cut some nice holes in it to get some cooling to the CPU. There is a good chance that there is actually room for a cooler and a fan on this card inside the A1200. But as you say I would probably chuse the 060 CPU instead as it runs much much cooler and the price/performance is much better.
As for you 030 running hot att 50Mhz that's normal... Those chips are made to fry eggs on I belive. My Blizzard1230 ran extremly hot but I still had the trapdoor closed and it never complained for all the years I've used it so there's probably nothing to worry about. :-D
