Disabling menu item and clearing caches causes menu item to become re-enabled

That is interesting, I will test. This might be do to the fact that the blog menu item comes from a view. Alternatively you could disable the view or module, which is not ideal. I would think that it would respect the menu setting.

I can recreate the problem. I think it might be a core problem. The work-around is to go to /admin/structure/views and just disable the blog view. That will disable the menu link as well.

Going to test again once I have a new D8 build to see if I am still seeing this problem. If so I will probably create an issue in the core Drupal issue queue. Tagging this as minor since there is a workaround.

I am going to place this in the Features queue to see if this has any merit as a Features bug. I don't think it has anything to do with OpenChurch which is basically just a collection of Drupal feature modules. It has to be an upstream issue, either in D8 Features or in D8 core.

Yeah, I don't think this can be features, since we're just bundling configuration.

Yeah I would suggest you to create an issue in the core queue describing exactly what you see, and what is the problem.
This could be a bug in core, but in that case handled there.

Moving to Drupal core. Closing as a possible duplicate of #2630776: Suhosin causes menu items to be disabled.