It's all to do with vagueness about the exact meaning of negation, opposite, etc. Necessary vagueness, because the world itself isn't black and white, so it's not always obvious how to apply 'disembodied' logic.
In the case of unwaning, as OP says, if it existed, the word would presumably mean not waning (i.e. – exactly the same as unwaxing, if we postulate such a word and sense).
The reason for this is simply that when we imagine the sense of unwaning we're likely to consider it within the context of a continuous oscillating activity, where negation invokes the idea of that activity not occurring at all.
The alternative, obviously, is to consider waning as one part of the two-phase process, giving waxing as the other.
This particular example covers just one of an almost infinite number of different ways things can be considered 'opposite'. Take loved, for example. Most people's first suggestion for an 'opposite' is probably 'hated'. It might take a while to realise that from a different standpoint, unloved is a more precise negation.
TL;DR: There are many different kinds of 'opposite'. The two in OP's example are perhaps the most common; reversal and absence (per @Hellion's comment, often indicated by un- and non-).