Hi, first: the version on Github is the development version and many of the filters and hooks there are not (yet) available for the table release.
So your case is an interesting one and clearly not something this plugin was designed to account for… There is compatibility with WPML (as far as possible) and Polylang which both have an option to redirect visitors based on language to their respective language homepages, but you seem to have a custom solution based on Geo data?
So, what is it that you would like to do? Simply remove the home page entry from being referenced in your sitemap? Or do you wish to replace the current homepage reference with the other geo-based homepage references?
To replace or add more homepages: the development version has a new filter ‘xmlsf_root_data’ which allows you to add or replace home page references in the homepage (root) sitemap. The current stable has a hook ‘xmlsf_url_after’ passing the argument ‘home’ in the homepage/root sitemap that you can use to output additional URL tags in the sitemap.
But if you wish to remove the homepage sitemap completely, I fear there is no such option in either the stable or the dev version (yet). I can add this to the feature requests but otherwise, you might simply have to create a redirect (in .htaccess for example) from your homepage sitemap to your page sitemap. This way, the page sitemap gets referenced twice in the sitemap index but I do not think that is a real problem – but if Google Search Console does show a warning, then please let me know ??