Yes it’s the same, the widget executes the shortcode itself, so it’s actually acting as if a shortcode was used within a widget.
I think you can safely remove that .htaccess rule, as it’s no longer neccessary for this version 🙂
Google crawl data can be delayed by weeks in my experience, but I’m not sure how accurate the report dates are to be honest. If you make sure that every cache is cleared, I believe these 404-s should disappear after the next crawl.