Works absolutely fine for me and I had this set up for a fair few years now. I use the original power connector to supply 5v/12v/-12v/0v rails and the floppy power header to boost the 5v/12v/0v rails.
A friend with a similar config to me powered his motherboard/accelerator only through the original power port and actually ended up fusing something on the 1200 motherboard after a few months.
