My A1200T motherboard is powered solely through the floppy connector. Works fine here :-)
Oh, if you're only supplying power through the floppy port you'll need to connect a -5V (usually blue) lead to the center of the original A1200 psu socket aswell - this is to make the sound work.
I don't know how safe it would be to power the A1200 from the original psu socket and the floppy connector at the same time.