The Datacom/AD Active Upgrade only backs up the CXX, DBIDs 002 and 015. Do I also need to backup the Autocollect system databases DBID 1018, 1019, and 1020?
There is no need to create backups for any other databases than those allocated by job AXACTALC. The Active Upgrade process updates DBIDs 002 and 015, re-creates version 15.0 base 1000 which holds the Dynamic System Tables (DST), and re-catalogs them to the CXX. All other databases, system or user bases, remain untouched by the Active Upgrade process.
Review the section Performing An Active MUF Upgrade in the Post Installation Process area of the documentation for the involved releases.