At which point and how to connect VNA on the PCB for antenna tuning?
I would connect the VNA to J3. It make it easier to perform measurements, and you can calibrate for the cable's length.

From your post, F1's input is not 50Ohm, so you can't connect directly to your device output.

J3 will allow you to orient the cable, to get optimal measurements.

The trace delay at 2.4GHz is negligible for BT.