So this, to my knowledge, is expected functionality. Home Screen Layout settings are not the same as App Removal settings, as it appears you've discovered. This is important for a number of use-cases, such as allowing personalized layouts while still forcing the presence of applications for troubleshooting or other reasons (e.g. I want every device to have TeamViewer QS installed but don't care if folks keep it on their home-screen since I can instruct them to swipe until they reach the app library view and search for it)
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