"Never keep all your guns in one place" doesn't necessarily mean to keep them strategically around the house.
Now, is this a 'good idea' to combat a armed intruder at a random moment when you're home? Yes.
Is it a good idea to have them around the house if a pair of buglers are tearing your house inside and out when you're not there? No.
When we really look at reality, anything is a possibility and if someone really wanted to take everything away from us, they'll find a way. The difference lies in how likely that is.
It's just a choose what situation you're preparing for. You'll have to be very creative. Me, I've outgrown the whole 'keep this and this gun in this bag, and this one in that bag' phase a few months ago. Just keep your main defensive guns near you at all times.
Thieves main target is the master bedroom. Albeit nowdays they'll target other bedrooms too, because of the large number of electronics, consoles and computers that are in those rooms now. So pretty much, they enter front door, try to access the master bedroom as quickly as possible, or if not, they'll find a bedroom just stocked with games and game consoles. This correlates with the two most common thing stolen from homes: Jewelry, and electronics. And I am pretty sure guns are number three. If you see a gun, you'd just take it if you were a thief. So in your house, make sure anything valuable, like a firearm, is not in this easy line that a person unfamiliar with your house will instinctively walk through trying to find your master bedroom.
The best method for storing anything that's valuable is in a large, thick dial safe that is bolted to the concrete foundation of the ground.