Hi Yannick,
temporarily I had to install one joomla instance in a subdirectory of root until a whole rebuild of the new website will be finished. Generelly SEF URLs are fine except ht "home" URLs.
It is a multilanguage website and I tried several ways to setup the url but with the language switcher I do always receive interferences to other urls than the base url.
The urls should read xy.com/subfolder/at/ and xy.com/subfolder/de/
Using the language switcher I do alway receive alias added to one of the urls. The hreflang reads the same. Like xy.com/subfolder/de/ refers to xy.com/subfolder/at/xyz
I found this configuration with no success. https://joomla.stackexchange.com/questions/4264/multilingual-associations-single-articles-for-home-page-duplicate-home-url
I found one ticket here where you describe to change the joomla settings in SH404 in regards to the alias handling with no success.
Your help is very much apprechiated.
Best regards
Peer