With my iPad Air 2 there is no reason to remove the Smart Cover ever. To be honest with around 5 years of iPad and 7 years of iPhone ownership.....make that any apple product I have ever owned, never have I had a cover that I needed to remove due to design, that being being the difference between well designed cover and a dock.
Just from habits, and user experience of owning apple iPads, the natural response is to fold the Smart Cover behind the iPad if I go portrait. The user experience should not change, the fault is with the smart keyboard cover and its design, apples answer to the kickstand.
Guess we are different . I've never seen the need to remove the Smart Cover off my iPad Air, it provides protection when closed and grip when used in portrait for me.
I tried the Smart Keyboard at the store, and like you, I did not like the way it folded, and I also disliked the additional weight it added to the iPad Pro. I ended up deciding not to get a Smart Keyboard, and got the Smart Cover instead. By the way, you seem to use the two names interchangeably, but they are separate products. I paired the new Apple Bluetooth keyboard with my iPad Pro, and I use that when I need to type extensively. Otherwise I just use the on-screen keyboard on the iPP. I'm using the on-screen keyboard right now to type this post. The iPP Smart Cover works exactly the same as the Smart Cover for previous iPads, and the new Bluettoth keyboard is very light. My plan is to use the iPP mostly at home, but if I ever need to take the iPP out of the house, I think I could throw the keyboard into a slip cover and throw it into a bag along with the iPP and it won't be much heavier than the keyboard cover, or much bulkier. To me, combining the iPP with the Bluetooth keyboard is perfect.