I don't know of any improper placement of the encoders. There were over 6 years of PPM testing in Philly and Houston prior to the first currency reports. By then, there was a fairly detailed set of instructions on how and where to install the encoder. Generally, it was the last thing in the audio chain before the Optimod or Omnia (or other compressor / peak limiter).
There was discussion of putting the encoder at the studio, ahead of the STL, with the Omnia or Optimod at the transmitter, as opposed to putting the encoder at the transmitter after the STL. Some of this discussion was about accessibility as opposed to effectiveness.
The PPM only went in the top 48 markets, and the roll out took the better part of two years. In general, those were stations that had big market engineering skills on the staff, at least in the stations that mattered. And, since the 50's stations of all sizes had, Sta-Levels, LevelDevils, Audimax and Volumax pairs and then everything from a bunch of LA3-As with a crossover feeding an Optimod to Compellors and Omnias. There was some form of AGC / Leveling followed by Compression / Peak Limiting at essentially every station.
There was always concern that the less dense the audio, the fewer encoding opportunities would be available. So along came the Voltair, which "enhanced" any available audio on the set of tiny frequency bands that the PPM encoder could use to insert the code burst. The only problem here is that, set aggressively, the Voltair brings up unwanted noise and/or artifacts that lie in those little audio slices, making the station sound very strange.
There can be as many as 12 to 13 PPM code bursts a minute in dense material. The issue is when the program material is not dense enough to allow encoding for long periods of time. It only takes 5 detections in any 5 different minutes in a quarter hour to get credit (actually only 3 in some cases given the "missing minute" rule) but stations fight for every one of those detections.