I’ve never tried that, but if I understand it correctly, you basically have a single Kirby installation, only your /site, /content, thumbs/ and /assets/avatars folders contain subfolders for each domain, e.g.
/site/domain.one.com
/site/domain.two.com
/site/domain.three.com
etc.
You need to provide a site.php with the code as laid out in the example. Kirby then automatically fetches the right stuff for each domain.