That's exactly the problem. Because Pioneer was spin-stabilized, it didn't need to fire thrusters, so the noise wasn't there and the anomaly could be measured. Voyagers aren't spin-stabilized, so they have to fire thrusters quite frequently. That makes it impossible to measure a small enough effect on them.
If they can measure the drag caused by radiation, you can bet they can account for solar effects.
Also worth noting: The thrusters are fired very infrequently. According to that page, the Voyager missions required constant adjustments but the Pioneer system is spin stabilized.