>> I have no idea which bike is where today. In photos, the Belgian bike looked real enough, discounting the repaint. I suspect it is the real one (or a good replica).
I'm almost certain that the Belgian bike (which is now in a glass case at a metro stop in Brussels) is the real one. The bike has been redecaled and the handlebars have been drilled, but three significant details appear on this bike and in the hour record photos that do not appear on the bike in the Colnago Museum:
Handmade Pino Moroni titanium stem Black headset Milled chainring
>> A second bike did not feature most of the special components and served as a backup bike.In one photo, Colnago is standing with this bike on his shoulder, while Merckx is circling the track.
There's another photo of Ernesto with that bike over his shoulder and Eddie next to him with his hand on the front tire. It looks like this bike is definitely the one now in the Colnago Museum... as you said it does appear to have different geometry and different components than the one Eddie rode.