I have always favored a one-to-one mapping between Perl distributions and version control system (VCS) projects.

Multiple distributions inside one VCS project might sound appealing for a tightly-integrated set of distributions, but I suspect could lead to problems later. If and when I feel the urge to combine distributions, I make one distribution (in one VCS project).

Splitting one distribution into pieces and putting each into different a VCS project sounds like a recipe for disaster. If and when I feel the urge to split a distribution, I make multiple distributions (each in its own VCS project).

Most platforms running Perl today have plenty of disk space. Unless your modules are for old computers or small embedded platforms, I would put them all into one distribution (in one VCS project).