I think the reason why the game does what you've described is because the PvE-only skills have "Attributes" invested in them (meaning you have a certain rank in the PvE-only skills' line(s)). Let's say you have no Attributes spent in Domination Magic, but have one point in Inspiration Magic. Skills under the Domination Magic line won't be expanded, but the Inspiration Magic skills will.
Personally, I wouldn't mind something like this, especially under the Quest Log, but I really don't care one way or the other. I don't think it'll hurt the game, but at the same time, it won't make it any better, just more convenient, so whatever.
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