Yes, ideally, every version of software that changes any external data format (e.g. of config files) should always accept both new and old versions.

But, unfortunately, some software does not, and it still needs to be packaged.

True. And the only effective solutions I can think of are extremely ressource intensive (man hours) and therefore unrealistic. (Lile wrapping non-compliant apps and using mandatory access control for enforcement)

And then you have moved stuff around and solved absolutely nothing, but you have created a new, permanent surface for security issues.