Why does the phase difference change after swapping elements that are in series?
The resistor and capacitor are in series.  This means (assuming the probe impedance is negligible, as it should be in the sim) that the same current is passing through both the resistor and the capacitor.  That is not changing when you switch the two.

You are measuring voltage relative to ground (i.e., single-endedly).  The reason is that you're measuring the voltage and phase as different is that in one configuration, you're measuring the voltage across the resistor, which is in phase with the current.  In another configuration, you're measuring the voltage across the capacitor, which is 90 degrees out of phase with the current.  In fact, in both cases shown above, you can see that the phase moves 90 degrees, or 1/4 of a cycle (2.5ms) when you switch which element you're measuring the voltage across.