Its not really that hard to cut out the extra pieces inside the UGC even with an Xacto Blade so i don't really see that being a problem. I had the same idea and in fact I'm already doing this in some ways. I've used the UGCs for housing my portable systems, extra cords & some controllers. You can kind of get an idea of what systems fit inside them from one of the pictures below.
I don't have any of my boxes for my systems (they are in storage at my grandparent's house). If i did have them i would have already scanned in the boxes and made some inserts for the portables i have.
Here are some of my portable in UGCs lined up (taken w/ my phone)

Here is the inside of the case thats housing my NDSlite w/ the power cable


The cases are really nice for storing any sort of things. currently use them for my portables, SNES controllers, NES controllers, GEN controllers, GBC trading cable, PS3 sensors for my guncon, PS1/PS2 memory card reader for my PS3, etc ... the list can go on forever.
