Then what about temporarily placing a 50ohm resistor where C9 goes (terminating the green 50ohm trace into a purely resistive 50ohm load), and, using the U.FL connector in its intended spot, you tune the antenna for a reading of 25ohm on the VNA. When the antenna is 50ohm, it will be in parallel with the green trace which is also terminated in 50ohm thus putting two 50ohm loads in parallel at J1 to give a VNA reading of 25ohm. Once you disconnect the VNA and remove the resistor from the C9 pads, the beginning of the green trace should present a 50ohm load for the matching network. To test everything afterwards, once the 50ohm resistor is removed from the C9 pads, your VNA at U.FL should then read (50-j[whatever capacitative reactance the green trace adds looking north]) rather than 25ohm, which will then be correct once the green trace is connected to the radio by installing L2 and C9.
If you really want to get serious, you could also have a spare U.FL connector handy so that once you do an OSL calibration to the end of the coax, you can then clip on the free U.FL connector and do a port extension to eliminate the minor effects the connector may have on the reading at the trace itself. However, I do believe we are getting too fussy as the matching network C9 and L2 will likely be standard value parts and not offer a perfect match to 50ohm anyhow. Also, the size of that connector is completely insignificant at that frequency and you could remove J1 without complication if you wanted. Remember, a 1.5:1 SWR will have no noticeable effect on performance, so I would go with simplicity over chasing perfection here.