I've just lived with the fact that I can't track changes to binary file formats through a version control system, but I use it anyway since it is useful. Note that typically most of these types of files are work products that will be released (user guides, docs, etc.)
For early project artifacts like requirements and initial designs, I tend to use text documents - not because I can track changes, but because I like to use my IDE for it.
I have never really been "bitten" by the fact that a change can't be "diffed" in version control. The commit comments and other documentation guidelines around changing an important binary document usually make up for that lack of visibility - in that there is another trail if you look for it.
I agree this is not ideal, but I don't think it is really worth fretting over.
Perhaps I just got used to the idea of a set of files I would be able to track as much as I would like.
I put a lot in version control, but also use defect tracking for some things with lifespans that are temporary.