We build our own Magnolia WAR project with custom modules. We added the magnolia-site-app to our project after we had already upgraded to STK 2.9.3 and found that we had to manually change config:/modules/site-app/apps/site/subApps/browser/contentConnector@rootPath to /modules/multisite/config/sites for our multisite setup.

Also, STKModuleVersionHandler removes the legacy Site definitions and Themes entries from the STK app launcher group when the site-app module is installed when upgrading to STK 2.9.3, but in our case the site-app module was installed after upgrading to STK 2.9.3, so this didn't happen and we also had to remove these legacy entries manually. Maybe it would be better to have SiteAppModuleVersionHandler take care of this, so that this also happens when adding the site-app module later on.