Could you clarify whether this same logic/behavior also applies to the restart that happens after plugin installation (when checking the "Restart Jenkins when installation is complete and no jobs are running" checkbox) or when clicking the Restart Safely button under Manage Jenkins (i.e., the /safeRestart URL
Both of these situations use the /safeRestart URL behind the scenes, which puts Jenkins into the same state as "Prepare for shutdown", which prevents new builds from being started and causes Pipeline builds to pause. The difference between /safeRestart and "Prepare for shutdown" is that safeRestart will also automatically restart Jenkins once all non-Pipeline jobs have completed and all Pipeline jobs have been paused, whereas "Prepare for shutdown" does not actually restart Jenkins.
Even before Pipeline: Groovy version 2.78, once Jenkins restarted due to /safeRestart, all Pipelines should have resumed automatically, and they should continue to have that behavior in Pipeline: Groovy 2.78. If your Pipelines are not resuming after the restart, please open a new ticket, including steps to reproduce the issue from scratch and any messages from your Jenkins logs or Pipeline build logs that seem relevant.