I just added a symlink from the « expected » path to the current path :
ln -s /home/yunohost.app/transmission /home/yunohost.transmission
(Which is a link to a link, as /home/yunohost.app/transmission is already a link to an external drive).
I also used chown to make all files/folders belong to transmission:transmission (even the 2 links, with -h argument for chown)
Then I restarted the tranmission service, without success.
The strange thing is that now, when I check the path for a torrent, the file is exactly where it should be.
Really strange side-effect : all films that were also added in jellyfin (with symlinks too) are considered not found (well, not 100%, more like 90% removed from library, 10% still in library, but unreadable)