I think that part of the appeal of an app like this is about keeping things "tidy". MacOS seems to be built around making it easy to clutter -- lots of randomly sized overlapping windows (resolved using Rectangle for Aero-snap like functionality -- the weird full-screen split-screen nonsense in MacOS is just frustratingly limited and slow and has too many animations and transitions to be useful), dozens of apps filling up the dock, six hundred icons in the menu bar (which I use vanilla.app to resolve), and so on.
I think my mental model distinguishes between applications and utilities. Utilities are effectively like the old TSR tools -- you start them, then they just run quietly in the background until you need them, with no interface. Applications, by contrast, _are_ their interface, so it feels strange that when I close that interface, the application itself isn't closed. This utility alters the behaviour of the OS so that it conforms to this mental model. I suspect that this is a situation where there's no "right" approach, but rather a set of preferences and learned behaviours.