And of course, having written one of the "Madeline didn't really die" stories myself, I am in complete sympathy with your choice to assume that her death was no more 'real' than Michael's! :-)
I also like the way you paint the picture of Madeline's increasing isolation, and the way this gradually undermined her ability to function well in her draining position.
That last point raises some questions about the way the Agency -- and by extension Jones -- managed its personnel. I think it would be natural to expect that people in high-pressure positions like Madeline’s might be vulnerable to exactly that kind of stress-related impairment over time -- the failure of Center and Oversight to put into place methods of detecting such problems and intervening to provide assistance is just as bad, in my opinion, as the similar criticisms raised against Madeline and Operations in the way they managed their own employees. In both situations it led to the organization squandering resources that they could have, with better management, saved.
I know we've talked before about this, so yeah. Word.
One of the things about Section that peeved me from the very beginning was their wasteful approach to their human resources. In S1, there don't seem to be all that many layers above Section, by the end of S5 there were many, and they did absolutely seem to have exactly the same attitude, which does suggest that Madeline and Paul simply operated within the system rather than created it. I have trouble letting Paul off the hook in this way, but I am trying. ;-)