According to this Desktop App support page, I can disable the Use Standalone Window For Phone Calls option in Settings. You can see by the below image that the option does not appear in my Desktop App Settings.
How do I disable the Use Standalone Window For Phone Calls option?
in the top right corner of the app there is a slider that says "new layout"
If I turn it OFF i see the option you want to disable.
If I turn it ON the option is not visible.
So you have to switch to the old layout, change the setting, and if you want you can switch back to the new layout.
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