Domain mapping and sitemap url

we are using domain mapping plugin on a multisite, we have a sub site (folders not sub directories) that has a mapped domain. We are using Yoast for wordpress for SEO to create site maps, but the site maps are showing the network domain as the main url: networkdomain.com/subsite/blahblah

If we change the Administration Mapping to "mapped domain" instead of "original domain" will that change the url of the sitemap? It seem that having a site map with networkdomain.com/subsite/blahblah can't be good for the SEO of the subsite...