The difference between The Daleks Master Plan and Prisoners of Time is: Daleks Master Plan episodes lead into each other. The events of episode 2 only happened because of episode 1. Prisoners of Time stories do not lead into each other. Look at The Body Politic (comic story). Which part of it depends of Cat and Mouse (comic story)? None. To be honest, it doesn't depend on any story before that.
In fact, I believe another analogy to this may be Series 5 (Doctor Who 2005). Most (of not all) stories on this season have tje presence of an enemy (the cracks in time) featured on the episode. 13 episodes. 13 stories.
Look also at Season 8. 5 episodes, 5 stories. All part of a season-long arc of the Master.
Prisoners of Time, in the end, is nothing more than a 12 issues arc about Adam Mitchell's revenge.