I can't think of any way around having the duplicated icons for the different division groupings. That just is what it is..if you want to use those ensemble presets, then you have duplicate icons on the stage, and if its all on one stage, then there they are. I really can't think of any way you can avoid that, aside from choosing to hide some of them once you get it setup.
It just kind of is what it is... If you never use the ensemble presets, you can just always use the individual players, which means you would need some way to divisi or unison the midi channels intelligently before sending to VePro. You can make a scripter script for that, or I am lately experimenting with using Kontakt as a midi plugin for this using the MultiScript divisi scrdipt that is out there floating around. Not super straight forward.
A much more simple script would be to simply say Track A is meant for a single player, track B is meant for two divisions, track 3 is meant for all players...etc.. then a simple scripter script that will duplicate the midi notes to all the channels for each intended case. Very simple script, but it would work. But note that the midi traffic to VePro and through LogicPro would grow quite big and you may feel it in the CPU. As the other person suggested, by using a Scripter script you can also opt to add some slight delay differences easily to each of the 16 players and things like that but ultimately you will be missing some of the humanization features that VSL built into the ALL PLAYERS preset.
I used to want to have just a single MIRPro stage, but I have since come to the conclusion that it doesn't really matter if there are 1 or 5 or 10 MirStages, unless you actually need to see all the players (including the duplicate ones you mention), on the same stage to make sure they all line up each other. But CPU wise, no benefit to a single stage. A little bit tedious to change rooms and other global room values for each stage though, that is true.