FYI: After just throwing a bunch of stuff at the wall, I've finally come up with the following which does work, at least for apt (haven't tried update manager):

    Update-Manager::Always-Include-Phased-Updates;
    APT::Get::Always-Include-Phased-Updates True;

Note the lack of a ":" in the APT:: line. Putting a : silently causes it to do phased updates.