Ever go to a go kart track and notice that some karts are faster than others? They're all identical as far as the eye can see, but in reality tons of subtle differences pop up.

You can have spec bikes, but there no way they'll all be tuned identically, all have the exact same lubrication in all the bearings, all have the exact chain tension, all have the axles torqued identically. All the derailers built exactly the same... One bike will get inevitably have an advantage over the others.

Assign the bikes randomly, and swap them around often enough between legs of the races. The Tour de France is pretty long.