Long term I’d suggest developing a feature to add a custom hreflang tags alternate URL set on a page by page basis (under the WordPress Pages and Posts Edit screen).
Something as basic as a form box that’s added to all WordPress Pages/Posts where the hreflang tags code can be added and then loaded into the head section of the corresponding webpages.
Note to self, add this to Stallion Responsive, would make a nice feature to be able to add custom code to the head of specific webpages (update I created the hreflang feature, screenshot above).
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