It seems that when using the flexible publish plugin to trigger other projects doesn't hook into the Jenkins project ancestry properly. For example, choosing "Flexible Publish -> Trigger / call builds on other projects" and point it to another Jenkins job does not cause the target job to show up in the dependency graph as a child of the first project. Similarly the "block on upstream and downstream jobs" options in either job configuration doesn't respect the relationship between the two jobs.

Further, given the fact that according to the plugin wiki page the standard "trigger other job" post-build stage is not currently supported by the plugin, which seems to be the only other way to conditionally trigger other jobs based on criteria provided by the current job.