I've just come back to debugging and had come to the same conclusion as you, so I did more debugging trying to find what the common issue was, was it the SA or the impersonation or something else.... So apparently you can impersonate a disabled user and most things work. 
One our automated scripts disabled my user that I impersonate (our "service" user) 2 weeks ago, the only things that broke were fast-list and chunked uploads (somewhere between 250Mb and 300Mb seemed to be the limit where it broke).
Thanks for all your help with debugging things. Now to see if Google thinks its a bug that most things work for a disabled user that you can impersonate.