I still think it's an excuse more than anything. I haven't seen Apple charging any money for new versions of Safari, nor iTunes (yes, iTunes does allow access to the iTunes store which will earn them money from some users).

With regards to the accounting, it might have something to do with the new software being an integral part/feature of a new version of the product. I'm sure they could find some other way to be compliant without having to charge for the programs.