It should probably do something cleverer, but it'd have to be much cleverer, as this option only shuffles the children of the playlist where it's set

Please don't get rid of this functionality. I depend on the "Aways Randomize" to only shuffle the top layer for the way I normally use the player.

Also I should point out for the sake of discussion (clearly you know this as the developer, but not everyone else may realize it) that the "Always Randomize" is not the same as a shuffle. It actually changes the running order of the initial list, so if you turn on shuffle and then turn it off again, you get the same "randomized" list you started with. Thus you can "shuffle" an "always random" playlist (which will shuffle tracks irregardless of which sub-playlist they are in).