This is hard for me to follow, but I think I get it. Let me offer a different perspective, just because I've been thinking about it recently:
1. "Global Shuffle" seems like a really weird feature when you think about it. In MC, it makes MUCH more sense than in other players, but it's still weird. A master switch that shuffles everything you add to Playing Now.... Kind of odd. It definitely removes your options to choose exactly how and what is shuffled.
2. Shuffling playing now, by pressing the hot key (ctrl-R) makes a whole lot more sense to me. Add some stuff to Playing Now. Decide you want this particular stuff shuffled: Hit the button. What if you were playing a shuffled list and in the middle of it, you wanted to add a whole album that you want to hear *not* shuffled? No problem. Add to playing now (as next to play). Done. Can't do that with global shuffle.
Reshuffle remaining is also an awesome feature. If you add new stuff to a large list that's in the middle of being played, reshuffle remaining shuffles the songs that are left, including all of the new stuff you just added.
The main point here is control. Leaving all shuffle type stuff set to off, and doing it by reshuffle or reshuffle remaining always gives you complete control, and it acts consistently. I have a good number of linked tracks and I never see duplicates when adding songs to Playing Now and then reshuffling. They always group together correctly and don't duplicate.
Just my thoughts and experiences.
Bria.