This is not a problem. You can still compare either $] as a number or $^V as a string (or will it become a version object?) and it will give you correct results.

GNU ls has the -v option to sort 8 before 10, I also find that useful.

(OT: Did you notice that files of dos version x.yy are released with modification time x:yy am?)

Also, that would be an epigon of the version nubers of TeX and plain.tex, that converge to Pi.

And odd minor version numbers are only for development releases, so if you want that people use new Perls, you should not use version numbers such as 5.9.999.