From some light research - I think this may be included in a 3.4 release but it was omitted from 3.3.7 release, which occurred after the changes were merged to master. I'm not sure what the rationale for that might be, but I'd probably feel slightly more comfortable leaving our eigen in eups until there's a 3.4 release. It sounds like that could be within a few months. The eigen mailing list mentioned a 3.4 beta was close to being put out earlier this year.
A possible solution is to create an `eigen_cholmod`, which has this specific fix for jointcal. Jointcal could rely on that explicitly instead of the acquired one from conda (Right now it gets eigen transitively from afw it appears). Everything else uses conda eigen, until there's a release with the fix in it.