As a Mac user, I do not generally expect closing a window via the red window button to quit an app. With only a few exceptions (e.g., single window only apps like the Calculator), closing any/all of an app's windows will keep the app open; apps that remain open after their windows are closed generally take a click on the app's Dock icon as a signal to open a new window.
But I do expect that selecting Quit via the menu bar will fully quit the app. Respecting that Quit command is far more important than treating the red window button as a request to Quit.
A few times I've needed to restart my Mac to install a software update or finish installing a piece of software. Typically, these processes present the user with a dialog to trigger the restart, which, when accepted, causes the OS to quit all open apps. In this scenario, BaseX causes the restart to fail, because it will not quit when told, and the restart will time out unless you find out how to quit it. (I use control-C in the Terminal window where I ran the `basexgui` command.)
I hope this sheds some light on the matter. Thanks!