Hi
Does it make sense to analyse all language versions seperately ( /en, /fr, /es ...)
There's nothing special about a multilingual site, all pages are just regular pages. 4SEO analyzes all pages on a site, so it will analyze all languages.
generate seperate sitemaps in each language for Google Search Console?
All pages are already analyzed and those useful are included in the sitemap (sitemap-4seo.xml). This sitemap itself is broken down into separate smaller sitemaps: per language and with a maximum of 1000 pages per sub-file. But this is internally managed and you do not have to do anything.
There's only one single sitemap (sitemap-4seo.xml) and it's actually automatically submitted to Google and Bing (unless you disabled that feature).
Best regards
Yannick Gaultier
weeblr.com / @weeblr