A long shot, but KRTH might have used KGB's charts for those few months of 1964 and '65. Or KYNO's. Both were Boss Radio and consulted by Drake at the time.
I think you are on to something.
They probably checked record stores from the offset, but to do that you have to have a "base list" to start.
The PD would not ask about songs that they would not want to play (Lawrence Welk, take another bow) and would have to carefully nudge the store representative to name any hot movers or songs that were not asked about.
The "careful" comes from the fact that by the mid-60's we all knew that store reports were often full of hype. Stiffs were mentioned as movers because some record duck had said, "If you report Joe Shmoe's 'Silly Saturday Afternoon' to KHJ as climbing, we will give you a free box of The Beach Boys.
And the final chart often had texture-enhancing turntable hits programmed by the station but which did not sell.