Where to connect the VNA during matching network tuning
The VNA should be connected in one of two ways:


Connect the VNA directly to the start of the matching network and cut any trace before the connection point.
Connect the VNA at the output of the transmitter (like in my case), but compensate for the length of the transmission line between the connection point and the start of the matching network.


Basically, when you calibrate the VNA up to a particular calibration plane, any extra cables/transmission lines that are added after the calibration plane result in a signal delay that rotates the impedance measurement around the Smith chart, giving an incorrect reading. Ideally the VNA would be calibrated right at the measurement point, but if this is not possible, then the length of any test cables/transmission lines between the calibration plane and the measurement plane need to be entered into the VNA in order to compensate.

If designed properly, the trace between the transmitter output and the matching network should be at 50 ohms, and as such is equivalent to simply having a longer test lead between the VNA and the matching network. If the VNA is calibrated only up to the transmitter output, but the transmission line length between the transmitter output and matching network is not compensated for, the measured impedance result will be rotated and as such, any component calculations based on that will be incorrect.