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All of those mean that they are already done. Such as commenting is already turned off, the uploads folder organization couldn't be unchecked because it was already unchecked, etc.

Those are not "errors", they  are messages which tell you exactly what could not be done and then even suggesting why – which is, as Heather explains, because they are already done.  

The month & year based folder change requires a CHMOD permissions edit, and it warns that in the setup. No harm, just ignore it and change manually in the WP admin. 

As far as "comments still appearing" – there may be some confusion. "Turn comments off"  is for new posts only. You'll still have comments appear wherever you've had them before, and thiose would need to be deleted and turned off individually in each post to go away.

I'm sorry for the delay – I answered his within minutes but apparently never hit the POST button.

To be clear, there is no setting for making the form disappear in Wordpress. Your theme has hard coded information in single.php for posts, and page.php for pages that will show either the commenting form or the words "comments disabled". 

The WP settings are to either allow commenting or not, but the THEME files must be edited to get rid of the form entirely… Make sense?