There is no reason not to put the power connector into the floppy drive connector, especially when using a Blizzard PPC. At least the 040 models of the Blizzard PPC boards needs a lot of power on startup just to get the board up and running. The more power the better as I see it.
On my A1200 tower I supply power to the motherboard through the normal power connector, through the floppy drive power connector as well as the P8 and P9 connectors on my Mediator board. Furthermore the Blizzrd PPC is powered directly from the PSU as well.
