I used CVS to update my version numbers, and indicate in Makefile.PL which file to pick the version number from. But I got so tired of Perl and CPAN thinking that 1.10 was an older version than 1.9 (where as CVS and many other tools don't). And then we got version numbers, qv, v-strings to make things even more confusing.
So, many years ago, even long before git became popular, I ditched using dotted version numbers for all my Perl projects, and went to DNS style versioning: YYYYMMDDXX, where XX is a two digit sequence number, reset to 01 at midnight. This hasn't given me any problems, and unless I start releasing more than 99 times a day on a single project, or hopping westward into "yesterdays" timezone between releases, I don't expect it to give me any problems in the future.
It also doesn't raise false expectations based on version numbers.