The NASA Horizon JPL web page accounts for that. The Horizons database is the result of a massive highly granular calculation of every known body in the solar system, using solar system baricentric dynamical time, which differs from dynamical time (now called Terrestial Time) only by milliseconds due to effects of relativity. Results are translated to Terresital Time or UTC on output.
The results are valid for an observer at the center of the earth who is using a clock beating at the same rate as an ideal atomic clock at sea level. The descrepancy is NOT due to relativistic effects. The measurement is the time measured on the sea level surface of the earth if, in that coordinate frame, a light pulse had been transmitted such that it would arrive at the point where the observer was when it was transmitted.
Voyager tracking is very clever. All communications recieved by Voyager are phase locked and frequency translated and sent back to earth. This removes most of the phase noise and frequency drift from the transponder. The transponder “reply” is recieved by deep space stations in Madrid, California and Canberra. Long baseline interferometry gives excellent angular accuracy and the phase locked transponder gives nearly ideal Doppler and ranging-time performance. The point where Voyager was at the time of reception relative to the receivers is a relatively simple calculation.
“...calculation of every known body in the solar system,...”
Then it must be because of Dark Matter.........or Climate Change.........or Trump’s fault......