Seems to me like it's a case of them simply heading down a path, and continuing on that path even if it's not quite the direction they should be heading.
They started with a pretty basic pre-snap system, and have added things over the years, and now we are where we are.
Like I said above they can streamline some of this stuff, to not only make it easier to manage, but also to make it better and more realistic. I think they'd be better off with basic core concepts for pre-snap, stuff like: bluff blitz, shade/press a specific receiver, line shift, etc. And have these core concepts be what pops up on the presnap menu. This would allow the user to ask himself as the play lined up: what can I do to augment this play so that I have the advantage?
Then on offense you'd have core concepts to counter the defensive ones, stuff like: hot routes, blitz pick ups, etc.
I know much of this already exists, but it's just done in a peculiar way. You have to go through excessive amounts of menus just to do simple things, and as your article notes it doesn't always mesh with the play call.