You would be the first to make such work that I would know of.
It's your board, your choice and your roll of the dice. At least replacement motherboards could be cheap.
In closing, the AGP power supply chips, capacitors, resistors, inductors and such should also be absent. Even as a embedded hardware designer, getting all the proper parts and more would test my patience and certainly I would not do it.
I have an older proprietary HP P2 mobo standard atx form factor that has no agp, however there are provisions for one on the board. In other words all the solder points and traces are present with the area outlined to indicate where it would be installed. I am thinking of installing a slot on this board myself. The board has an onboard agp, but the bios has no setting to disable it. What would happen if I did this?