Finally got it to work!
So the process is:
Place your .dat and .json on the server inside a folder called "cache" In the markdown panel Data, don't use the StartURL property. Instead, place the full URL in ServerUpdateURL but without /cache folder (so something like https://www.mywebsite.com/doc/ , not https://www.mywebsite.com/doc/cache/)When the binary is launched, the doc will be downloaded from the server
However, there are still a few little bugs:
If you update the doc on the server, it will be updated at the next init in the AppData as it should, but the doc won't refresh until restarting a 2nd time (might be the index that doesn't rebuild) The "Update documentation" button doesn't work in binary The hamburger button to show/hide the TOC is invisible (but clicking works, so it might just be that the path isn't embedded)