I would guess that Unity Gain is techically different than Bypass. IMHO, bypass would suggest a direct, alternate path from input to output, whereas Unity Gain is the normal path with zero attenuation/amplification of the source signal. This arrangement allows the downstream main power amp to "see" the same signal that the upstream processor will be sending to the other amp(s) for the remaining channels.
So while it's technically different, the outcome is practically the same. As Dave suggests, if the BAT is capable (transparent, resolving, etc) of producing high quality two channel, then it should be satisfactory in a home theater signal chain.
For disclosure purposes, I have a BAT VK-3i running my dedicated two-channel rig (BAT power, Magneplanars).