Do gene expression levels necessarily correspond to levels of protein activation?
It has been well established that mRNA abundance serves as a poor proxy for protein abundance in most cases. This paper on yeast and this paper on cancer both establish this, although using older techniques (SAGE and microarrays, respectively), while this more recent review discusses the topic in light of more recent technologies (e.g. RNA-seq).

Perhaps the difficulty with exploring the correlation between mRNA levels and levels of active, mature proteins is that we still know so little about so many proteins and and what makes them active and mature versus inactive, premature, etc. Not all proteins need post-translational modifications to be active, but some do. Currently, this is investigated on a very detailed protein-by-protein basis (as far as I know), so gathering enough data for a large-scale study could take a long time. On the other hand, there are a variety of (increasingly affordable) high-throughput methods for measuring the abundance of thousands of RNA species simultaneously. I think people are using mRNA levels to estimate expression not because it's the most biologically cogent course of action, but rather because it is much easier, more affordable, and more high-throughput (which is all the rage these days).