The holster was an idea I was going to bring up with you, given the nature of your post.
I'm somewhat leery of leather for storage, even with stainless steels, I've found that it's a matter of when more than if, even with dessicant and surface-protection on the steel. Ironically, the flip side of that is that leather holsters are also oftentimes the most form-fitting, which is, of-course, excellent for storage.
Would you consider moving a size up in terms of the container/packaging and going with modern thermoplastic holster? Blade-Tech used to carry IWB and OWB options for the CW45, but I think they discontinued them (although I believe that new old-stock is still readily available from some retailers). I'm sure that most of the Kydex-folding shops still have these molds, though.
In answer to your follow-up question:
The handgun for my go-bag is actually my range/training full-sized XDm9, which allows me the ability to share common magazines with my EDC (XDm9 3.8 Compact). Much like your setup, it is in a dedicated container of its own.
This handgun bag is slaved to my go-bag in a removable manner. The reason for this is because the go-bags for our family are configured not for the zombie apocalypse, but rather for the more likely natural disaster evacuation. Given that municipal shelters are not likely to allow weapons, the ability to quickly and discretely cache the gun without the need to dig through the main bag is something that I had to consider, no matter how unappetizing that thought might be.
I don't have a picture of my setup, but it is quite simple. It's just that gun in a PHLster Floodlight IWB (w/Surefire X300U attached), 19+1, supplemented by three more 19-round magazines. The rule in our house is that holstered guns are always ready-to-rock as soon as they clear the rig, versus unholstered weapons, which require chambering. As a result, the ability to store the gun in a holster was a big consideration for me.
Our bags are a bit unconventional in that it's designed as a family unit, with only basic but common (i.e. identification, communications/power and lighting, self-defense and basic multitool, trauma/first-aid/individual meds/hygiene, navigation, money, water purification/fire/food/shelter) individual gear supplementing each bag. This allows us to be able to have a lot of shared resources as a family unit - for example, a part of my wife's pack is dedicated to more advanced medical resources because she is a physician, while that space in my daughter's pack is alloted to extra food to sustain all three of us - while still giving each individual the ability to get by for a shorter time period, should we be separated.