I feel that this single-pane-of-glass approach works better for some folks' mental models

That’s a fair question but I can think of one big advantage of going this way and that’s to do with distraction-free workspaces.

To use a comparison, have you ever picked up your phone to enter an TOTP / one time auth code and then accidentally found yourself texting a friend, or some other non-work activity. It’s particularly easy to get distracted if you have an open notification you didn’t see until you went to use that one time code on your phone.

Having a desktop app for your workspace helps hide Slack and other distracting items while context switching between different productivity apps.

Window layout isn’t the key feature, creating a spatial map of open files and other resources is.

I conceptually agree that managing windows should be the task of... the window manager, but at the same time it's easier and lower friction to both develop inside of an app and get some user to test new features

agree , it should be WM isntead of a very limited electron app.

Because native virtual desktops still mostly preserve app windows, not project context. Cate is more scoped: one workspace per project/folder with terminals, browser previews, editors, notes, agents, worktrees, docked tabs/splits, and restored panel positions. It’s not meant to replace GNOME/KDE/macOS/i3 globally, more to keep the messy project-specific layer in one persistent place.