It shouldn't affect your Google listing. Since this mod only generates a sitemap of your store - having the sitemaps files in the root of your store (/store/*.xml) is perfectly fine. Google will be able to use your sitemap to find everything that exists in the /store/ directory or deeper.
If you were to manually add urls into these sitemaps for locations in the root of your site - or any folder at the same level as /store/ - it would not be in accordance with googles requirements and probably not be indexed. But... if you were to manually add locations like these you might as well just create a new sitemap, put it in the appropriate directory, and register another sitemap for your site.
and to ramble on further... with your current sitemap location, any files located here (and any folders inside of here) will be indexed just fine: rubberduckbathrooms.co.uk/store/
In those same sitemaps located in the /store/ folder any urls to places like:
rubberduckbathrooms.co.uk/index.htm
rubberduckbathrooms.co.uk/somewhere/myfile.php
rubberduckbathrooms.co.uk/somewhereelse/anotherfolder/abc.php
are NOT valid.
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