Freezing game-time while in inventory (and possibly other screens) will allow players a method to stall game-time whenever they want. The menus are transparent in the NotEYE versions, so you can still see the play-field, and consider your move without the intended auto-moves of challenge mode.
I tend to agree with JellySlayer, in that is may sound like a simple change to implement at first, but the massive complexity the menu system has evolved into over the years makes it hard to do in a way that's playable and/or can't easily be worked around. Of course the menu system could be completely re-written, but that's just going to alienate you from the player-base already familiar with the current system. And to what end?
I think this is one of those ideas that's nice to consider, but probably impossible to implement without gutting and re-designing the game UI -- which I'm certainly not in favour of.