I know it's probably a bit late to come to you with this, but for the benefit of whoever browses this in the future, the MF A3.2 integrated has been slightly upgraded.
Certainly the version I demoed initially is very different from the one I got from MF, new. I got my A3.2 integrated amp about a month ago and there are several changes to the one I was demoing. For instance, the front power led used to be an irritating red light, and now is the same blue of the others. Furthermore, the remote control steps to change the volume level, which were naggingly large, are now a lot shorter, making the remote control of sound levels effective.
One of the instructions on my new amp was indeed that it has a particular input (Aux2) that is designed to be used with home theater settings, and lets the sound pass through transparently.
I don't know from when MF started to ship this version of the A3.2 but for sure now they have this bypass option.
Hope this helps,