If the wind up is returned, would it not be returned in the reverse direction?
Imagine a bike with only a crank on one side and this becomes obvious. Could this affect forward motion and if so by how much?????
Think of it this way. Let's say you are cranking out of the saddle and are the the non-drive side down stroke, from 9 o'clock to 6 o'clock. Moving the crank through 90 degrees of rotation, 60 degrees of this rotation is transferred to the rear wheel, and 30 degrees is "wind up" in the bottom bracket (so now the crank arms aren't parallel anymore !) . At the bottom of the stroke, at 6 o'clock) you aren't exerting anymore torque so the bottom bracket springs back and moves the crank arm and your foot back to the 7 o'clock position. You now have gained the spring energy back in the form of potential energy in the lifting of your leg and body center of gravity and can now let your weight fall the extra 30 degrees to gain back what you put into stored spring energy.
The point is that energy is not lost in this system. The work you do winding up a spring is "done back" on you during "unwinding".
PS just for grins I calculated the following.
A rider exerting 750 Watts of power (huge !) at a cadence of 80 RPM is exerting an average torque of 66 foot-lbs on the crankarms. This torque will twist a 110 mm long, 0.625 inch diameter solid Cro-Moly cylinder (like a campy bottom bracket) through an angle of 2.4 degrees. I seriously doubt you can even feel 2 degrees of crank non parallelism.
But for the sake of comparison a 1 inch OD, 0.875 inch ID hollow cro-moly spindle of the same length (like an ISIS BB) will twist 0.89 degrees under the same load.
So I guess you could say an ISIS BB is 3 times stiffer. But are those kind of angles significant? We're talking about one third of the angle that the second hand on your watch ticks through during one second.
Now on the other hand I think frame twist will be much more significant. But again this energy is returned to you.
Want a stiffer bottom bracket? Buy a frame with the shortest most monstrously thick chainstays you can find.