This shouldn't be a problem. Since folks are booting from CF Flash cards and microdrives, it will work with a CF-IDE adapter, since all the adapter is doing is changing form factors. In fact, I've read at least a couple of posts where folks have hacked up their CF slots and booted from them using a standard hard disk. One enterprising fellow even managed to stuff a 9mm drive into the chassis.
Your hard disk may show up as d: instead of c:, which could cause problems, but it should work. If this really bothers you, there is an easier way to solve the problem - disable the onboard flash disk. Find CEN and lift it - I know I've seen the datasheets on the board, but I don't recall where. I believe it is active low, so it *should* be pulled up internally. If it isn't, then find a pullup resistor on the board somewhere, and tie a jumper wire to it to force it high. With the onboard flash disabled, your CF slot will automagically become C:, even though it is logically disk 3.
IOW, while I respect a man that will wire 25+ jumper wires from test points to a hard disk - it is really unnecessary, as the CF slot will provide all of the functionality you need to connect a single storage device. I would say lifting one pin and running a jumper wire is much easier than building a connector and tack soldering all those lines to test points. If you want to use the CF slot to connect a CD-ROM, on the other hand, then adding all of that wire makes sense.