deleting system apps in recovery keeps them in running os

I want to switch from supersu to superuser, and having an interesting problem that supersu somehow covered up. I have a Nexus 5x running the stock rom. With every months upgrade I would flash using fastboot, go into twrp recovery before first full boot and remove a bunch of unneeded applications in /system/app. When I would boot up those applications would be gone. Somehow this isn't the case with superuser. I can still go into recovery and remove them, but when I boot up all the applications are still in /system/app. If I go back into twrp they are still shown as being missing. I've tried installing es file explorer, but it's unable to delete the applications once the system is up. remounting /system doesn't work either. Any help?

Unrooting supersu caused all the applications to come back; so does supersu not really delete them either, but somehow prevents them from showing up following the recovery scheme or something?

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