I think we must be using the term "balance" in different ways, as I'm struggling to make sense of your post, based on my interpretation.
In my interpretation, 'balance' would mean that no (class/skillset) has a clear competitive advantage over all others*, such that all options were equally valid.
There is nothing about skills-based games that would stop a particular skill/skillset dominating over the alternatives (swords do 1 million damage per hit, maces do 1 damage per hit with no other differences: clearly swords and maces aren't 'balanced', in this admittedly ludicrous situation).
Is your argument that this interpretation of balance doesn't matter, because, in the above example, anyone who used to use maces can just switch to swords and redress the balance? If so, I suppose I have to agree in principle, but it doesn't feel like a system which I would describe as "balanced" - while the players may in principle be balanced, skills and classes are not, and this leads to uninteresting gameplay.
* - Obviously class differentiation may lead to some classes being better at some things than others and so forth, but taken as a whole classes should have roughly as many good points as bad points. Exact counting of good and bad points may vary, but this should be the general goal.