I always publish the set of ortac packages (6 packages with dependencies among them) together in one PR on opam-repository. This never has been a problem. You may have to do the PR by hand / your own script rather than relying on opam-publish or dune-release depending on where are the packages.
(I don’t know about automatically publishing from CD).
I have two packages - CamlPDF and Cpdf, which must be synchronized. And it’s no problem to submit separately - we just make sure Cpdf’s opam file requires an equal version of CamlPDF - say v2.9 requires v2.9.
In some other package managers - say Fedora - special mechanisms are required, because it will always want to supply the latest version available. But not so with opam.