Attached are VENABLE TECHNICAL PAPERs # 16 & #18.
It explains that "The criteria for making a loop measurement was to find a place in the loop where the signal was confined to a single path and the impedance looking into the circuit input was much
higher than the impedance of the circuit output."
In your first example, one side of the injection point is hooked to the output of the amplifier (low impedance) and looks into higher impedance circuitry. This is done correctly. I always set up my simulation this way and the phase with respect to 0degrees is directly measured as the phase at crossover, without subtracting out 180degrees...which is nice. I like to see it this way.
In your second example both sides of the injection point are high-impedance, therefore this injection point is incorrect. In a real-world application the results will be compromised most likely. Seems to work in a simulation, but the phase is shifted for some reason...not sure why.
Either way, you just need to realize that the results are the same in your simulation when shifting the phase 180degrees as pointed out in the previous reply. You have a single inverting amplifier application here, so the low frequency phase shift will be 180degrees.