You're probably going to be better off, then, using an XML file.  That way you have complete control of what you store and how you store it.  If you're working outside the parameters of the normal behavior of the QSettings class, then the extra work to wrap data around your own storage system would probably be worth the effort.
You can always mimic the appropriate subset of the QSettings API, if you find it convenient to use in your code (as far as loading and saving values.)