@netgeek
I have gone back and forth from Fairphone OS and Stock several times during these first few days of testing and although I haven’t actually put two sims in the phone when on Stock, the second unused one shows just as on Fairphone OS.
So I guess that the answer is that even with Stock the second sim will work.
Stock doesn’t come with Google apps preinstalled and if you install Stock from recovery you don’t even have an option (unlike in Fairphone OS) to install them. If you install them in Fairphone OS and then use the updater to go to Stock, they will be waiting for you on reboot (read my post above for more details).
I think they can be installed in some other way, but I didn’t bother trying.
I don’t know how healthy a move can be to force the uninstallation of the Fairphone Launcher and the Peace of Mind app, but when you are on Stock you don’t have to worry about either as long as you don’t use them, and even in Fairphone OS you can just install another launcher (someone suggested “Launcher 3” from F-Droid).
So, to sum up, if you would want a Stock-like experience without G-apps, then just don’t install them and try the Launcher 3 on Fairphone OS and you won’t need to do anything else.