She's loyal to Jon and worried that Sansa might try to usurp his position.

How is Varys flawed? I would think he'd be one of the good guys.

Assuming R and L got married (somehow), Jon would outrank Dany even if he were female because R was Dany's elder brother. For the same reason, in today's British monarchy, William's children George and Charlotte are ahead of their uncle Harry in the line of succession.