Maybe that 3rd hole is where the stock foot peg position would be? Don't know.
I would put the pegs where you like them.
Just tack them on and check your ground clearance before fully welding.
One hole bolts to the bottom front engine mount.
One hole at the top bolts to the engine top front mount.
OR...I think you can bolt that top hole to the Honda frame triangle mount plate?
On a Roadstar Adventure.