By definition, bypass means that it does not affect the signal, so no gain control – sorry.
But, when the unit is in relay or dsp bypass it is unity gain, so should not change the level. This suggest that there is a problem with the way you have it connected. As far as I can see the Apogee has balanced line inputs, so make sure that the "hot" is connected to "tip" and both "ground" and "cold" to "sleeve" on the Space's output. My guess is that the "cold" is unconnected.
Essentially, if the unit is in relay bypass it is out of circuit, so if it is not passing the signal properly the problem is almost certainly at your end.
