I have personally fixed several client sites problems that were caused by doing this. The problems ranged from Google assigning penalties to Google deindexing the sites pages. If you know what you are doing then be me guest. I can only tell you what I have found and fixed in my own personal experience.
In this case, the www. site is not being indexed, nor was it indexed at any time (made conscious decisions from the start and stuck to them), so we're not talking about deindexing penalties. In my case it was crawling errors reported.
Still, if the non-preferred version of the site was being indexed, this does not seem possible to have been caused by the claiming of both versions of the site (with and without www.) in Google itself.
It sounds like it could have been caused by
- bad rewrite
- no rewrite
- change of heart concerning the use of www. along the way.
In this case, there would have to be deindexing.
Still, the option of making Google use only one of the versions of the site for the search results/links it presents to users is no bad thing and it can only be done if one claims both and explicitly sets the preferred one.
I cannot see how this is in itself problematic, unless one sets the wrong choice in preference settings, which is not that easy to do, i.e. it's not at all complicated.
If Google is not crawling the www site submission then this is of course a good thing otherwise you would be in the possible scenarios I mentioned above of recovering from Google penalties and scrambling to get your website pages reindexed after Google deindexed them. ;)
The crawl error is obviously not an "error" but a good thing. I doubt that you want Google to crawl the function.require file.
So we're good then! That's great actually, cause it saves me the worrying.
As I said my novice rationalizations interpreted this as a potential problem. Cause before the site was not being indexed either but this happened without (crawl) errors being reported, now it's still not being indexed, but it's reporting crawl errors.
I thought that might mean inefficient rewrite/redirection but I'd rather be wrong than right.
If the result is the same, I'm happy. The difference does still seem to be with how WordPress manages the www. version...is it the php rewrite making the difference between Joomla and WordPress? Let it be...
Thank you for answers, I know I have taken advantage of your good will and taken up much of your time.