I experienced the same thing. Without the extension but with these flags enabled, there's no way to bind certain hostnames to certain containers.

This is sort of documented in https://support.mozilla.org/en-US/kb/containers#w_what-you-c... #5. That page covers it but doesn't clearly spell out that the itemized features are only possible with the extension. As far as I can tell, the extension is called "Multi-Account Containers" while the feature is called "containers" and readers are expected to know the difference when reading that doc. (Suggestion to Firefox docs maintainers: if that's correct, change all occurrences of "Multi-Account Containers" to "Multi-Account Containers Extension")

Oh, I had never discovered that feature... So I won't miss it yet. Need to think whether that makes it worth to use the extension again. For now I just enabled the manual configuration and have not noted any differences yet.