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This is more a tech question for Mal or rbiii but I do recall the discussion that led up to the current configuration. The problem, as it was described at that time, was that when assembling a model from parts, rearranging the face order often interfered with transparency and as such it was decided that the ability to maintain ordered faces was needed. I also recall that I was mapping the "enterprise" for alphaville at the time and liked the idea that saving groups of faces rearranged the order so that groups were stored together, which was great for revisiting sections afterward, but that the current configuration removed that aspect of things.
Also, recently, I've been working on a couple models where merging verticies changed the face order and interfered with transparency, ironically, so I had to leave them unmerged. Fortunately, that isn't really a problem in the situation I'm working in, but I can well imagine it being a problem in some circumstances.
"Maybe" you could try resaving the model using a previous version of binedit (1.03?), it might regroup things to reduce the number of texture entries.
And that's about all I know on the topic.
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