Cyanogen installs bloatware automatically I'm using a OnePlus One, running Cyanogen OS 13.1 (build date June 16, 2016), stock, non-rooted.

I usually disable/uninstall all bloatware like a knee-jerk reaction.

But recently I've noticed that some of these apps re-enable or re-install automatically, namely Cyanogen One Note Plugin, Email by Boxer, etc.

How's this even possible? How may I disable/uninstall them permanently without rooting?
If the apps in question appears to be user-uninstallable but keeps coming back, they might be in /vendor and /system/vendor. But if they are only available for disabling, then they're real system apps.
Either way, you'll need to gain root to access and eliminate them. As you have pointed out, unlike CM, COS doesn't come with root, so it might pose a problem.