I wonder if it's actually anything to do with mentally mapping digital areas per se, or if it's more to do with the fact that you're not engaging your senses in the same way as when you're moving around a physical space.
If I go to a new place, say a gas station, there's a specific route I took to get there. There's smells and sounds and sights that will be specific to that time and place. I feel like that will generate a memory that's much grittier for the brain to hold on to, than one where I've digitally moved through a place. When I jump around a Quake map, I know where I'm going, but there's no wind in my face and I'm actually sat in a chair.
Sure there's sounds and sights in digital spaces, but they don't smell like anything and you're not actually touching anything but your mouse and keyboard. And the sights and sounds are less textured than real life - repeating assets, limited number of sounds etc. You're not gonna be surprised by a new birdcall, or a sudden burst of smell when the gas station guy opens the grill.
Knowing how important smell alone is to memory, I wonder if what's actually happening is that you're mentally engaged in a pretty narrow way when gaming, and that that's not really the best way for a brain to operate for long stretches of your life.