Hello,
1) If the plugin works fine with Storefront but does not display options on the single product page with our theme only then contact plugin author and ask what WC hook does he use to display these options? Maybe this hook is missing in our theme and we’ll be able to add this.
2) “is the latest update for xstore Version 4.9.4” – don’t understand your question. 4.9.4 – is WP version and XStore 4.20 is compatible with this version of WordPress. What another update you are looking for?
3) Go to Theme Options > Header Settings > Disable Header overlaps the content option.
Regards