For those experiencing the same problem...
After a lot of searching I was actually able to find the sitemap here: /@api/deki/pages?format=sitemap
So I redirected the /sitemap.xml to that URL by using a rewrite rule in apache2 config.
Edit /etc/apache2/sites-available/dekiwiki (in ubuntu)
Add the following rule somewhere after "RewriteRule ^/(.*)$ /index.php?title=$1 [L,QSA,NE]"
This will let the sitemap.xml be proxied to the actual sitemap URL in the api.
RewriteRule ^/sitemap.xml /\@api/deki/pages\?format\=sitemap [P]
Hope it helps someone someday.