The file health check error is not necessarily a problem, but it might conceal a real problem if you get too used to seing the message. It is not recommended to overwrite any core files as you might accidentally override them in the future with an update. Storing those images elsewhere on your server and changing the style properties and options as needed is the correct way to do it.
All my errors are in the addon.json files. (unexpected content)
Before I go any further, I did upgrade to XF2 b2 and not full clean install.
I am going to start a clean install see if that resolves the issue for me.