So if you have any channel connected via XLR, they all have to be? That sounds odd - I'd ask for a clarification on that one. It would certainly be highly inconvenient if someone had any reason to mix channels like we're discussing, not to mention the fact that it seems like they're almost making it harder than it needs to be by tying each channel's auto sensing together into a global behavior.
Killing the power on the rear panel should not cause the 990 to lose its settings, as those settings are in a non-volatile memory (hence the ability to retain settings across power outages - my old Model 950 remembered its identity even when it went 11 days without electricity once).
I could be wrong here, as we are moving beyond my usual territory, but I think that by "unity gain" he means basically a complete bypass of the 990 (including volume control, such that the "gain" or volume applied by the 990 is completely wide open, all the way at maximum). I honestly don't know quite how you'd do that with the 990, but there's definitely not an easily-selected option for this that would preserve the clean signal path you are trying to achieve with the ZD and A5.