I do know that as of VX2.4 if the Pour Outline does not cover the center (origin) of the pad it will not flood over it.
From your second to third pictures the clearance of the pour to the top pad of XR2 is different. The second picture has a much bigger clearance. That is at least part of the reason your pour is separating around that thru hole.
Yes, I had to draw a weird shape for the copper plane outline for the third picture to include the centre of XR2 pad.
For picture 2 PADS seems to be applying some clearance rule that shouldn't apply as it's the same net! In picture 2, XR2 pad already has plane thermal ticked even if it doesn't have a white cross on it.
All of this means that any pcb with a copper pour (and lots of our pcbs have them!) will need a lot of checking before we can use it. This is just very annoying and time consuming. Thanks anyway cbedard.