I’ve been using the pocket-sized CF flyboxes for the past few years, and while I’ve liked the micro-slits and the size, I can’t tell you how many flies I’ve lost due to the boxes not being waterproof. When I was fishing the Clinch a lot more, I fished chest-deep water often, and with my vest I was constantly dunking flies.
A bit over a year ago, I bought a couple System X boxes and started using those. I love the fact that they’re waterproof, and I dig the replacable “page” system. However, they’re just too danged big for the number of flies they hold, and they don’t fit in a shirt pocket. Also, hooks tend to back out of the foam and flop around, particularly the smaller sizes.
I have looked into what it would take to modify a System X box by manually cutting slots, but I never did it. Glad I waited, Scientific Anglers did it for me:

This is a smaller, pocket sized box based on the System X design, but with slits cut in the foam similar to the CF boxes.