Yeah, this is irritating. I don't think you can set it to give a 'flat' folderless view in the default mail app. There may be alternate mail apps that may work.
I've just altered my rules so that critical and time sensitive messages/alerts always go to main inbox, this may not be practical depending on the number and types of messages/senders you are working with.
Be sure to check your folder sync settings as subfolders will be set to manual sync by default. If a folder gets set to auto, it should still pop a notification on the lock screen, which can take you to that folder, but it won't show in the new message count on the app icon.
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A single player RPG featuring a branching, player driven storyline of meaningful choices and multiple endings alongside challenging active combat and intelligent AI.