Does it rise ... to the top of Activity Monitor's %CPU column when those messages are generated?
Not to my knowledge.
Something's got to be using CPU cycles when those messages are generated, and although it may be for just an instant, it should rise to the top of a
%CPU sort, i.e. make sure that the %CPU column is selected.
I've got same [osxupdcombo10.11.6 for El Capitan] in reserve but can't see the point in rerunning it since installing it originally just over a year ago. The current issue only first showed in December 2018 and so would not likely be due to a faulty installation of the update.
Like V1 has said many times (well, it's a paraphrase), it ain't broken 'til it is broken.
Just because that launch agent functioned properly
until December doesn't mean that it didn't become corrupted
in December.
I can't honestly say that that launch agent is at the root of your problem, nor do I even know if the Combo actually touches it, but rerunning it can't hurt. It's a, perhaps
the, tried and true troubleshooting technique (and your only other option may be reinstalling Yosemite in its entirety).