The way I see it, Multi-Account Containers has at least two use cases which it does a very good job at.
1: Keep cookies seperated between tabs. For example one container for personal use, one for work.
2: Different tabs via different VPN servers (SOCKS proxies). With this use it makes sense to enable "Delete cookies and site data when Firefox is closed"
I think it would be really interesting to combine these two use cases. By that I mean make some containers automatically clear browsing data, while others remember it.
Then you could have a setup like this:
Container A - No VPN, keep cookies.
Container B - VPN, keep cookies.
Container C - VPN, automatically delete cookies when closing Firefox.
I think the best way to solve this would be to allow for more fine grained controls over Firefox settings (like the "Delete cookies and site data when Firefox is closed" setting) in each container.
In the meantime, the best workaround I have found is to use "Firefox Browser Developer Edition" for one of the use cases.