Mine is working fine, I'll share what I did.
First, create your site as PHP (I used PHP 7.3):
wo site create doma.in --php73
Now go to /etc/nginx/common and make a copy of php73.conf to, e.g., php73-yourls.conf (that's because I'm using PHP7.3, you gotta adapt to survive).
Now edit the just created file (with vim, nano or whatever you use to edit configuration files) and make the line with try_files to look like this:
try_files $uri $uri/ /yourls-loader.php$is_args$args;
You must replace index.php with yourls-loader.php. Save it and edit your vhost:
wo site edit doma.in
Now you find the line where Nginx includes the php73.conf file and replace it with your own configuration.
Change it from:
include common/php73.conf;
to:
include common/php73-yourls.conf;
Save your file and you should be ready to go.
This procedure is way easier to do than to explain. 🙂