I’m not sure what exactly is causing this, but here are a few ideas of what you could try/check…
Have you ever tried without your tuning? Maybe it has something to do with the scheduling/priority settings you added or with the ExecStartPre option that checks whether apache is running.
Or maybe some app you have installed causes the job to fail, like in the following thread… Background cron jobs failing at regular intervals after v. 25.0.1 - #2 by n0plan
Also, if you’re using APCu as a memory cache, make sure that APCu is enabled for the CLI, otherwise some scripts like the ones in the cron.php tend to fail. See here and here.