You can measure the pH after addition of the mobile phase, and it will be valid if you understand a few things. First, the pH scale is no longer 0-14 with 7 being neutral. Any given organic/water mixture will have its own pH scale, with a fixed relation to the familiar aqueous one. This means that you can calibrate with conventional buffers, and still have a repeatable measurement of your mobile phase pH. Second, the reference electrode will have a different liquid junction potential depending on the filling solution and the organic/water mixture; fortunately, this effect is usually minor and you can ignore it. Third, the pKa (and thermal coefficient) of your buffer salt will shift in the organic/water mix. This effect can be as much as one pH unit either way.
There are a couple practical issues also. The liquid junction of the reference electrode may suffer from crystallization if the mobile phase is mostly organic. There are reference electrodes with more generous junction area that will work better.
If you attempt to transfer to another lab a method that measures pH after organic addition, be sure to specify the type of electrode you use. This will minimize the hassles for the other lab. The exact brand is not (usually) important, just the type.