Joe,
For a few years it seems to have been railroad preference. The wide cab Dash 8s (C40-8W) all had oval-shaped windows, as did the first Dash 9 (C44-9W and C40-9W) deliveries. To my knowledge, the rectangular windows started showing up on BNSF orders after the 900 and 1000 series models (Heritage I paint as in your link), i.e., the 700-series (BNSF warbonnet) and 4000 series and above (Heritage II) had the rectangular windows. (The former ATSF Dash 9s all had oval windows).
Subsequent BNSF GE wide cabs also have rectangular windows. Those would be the AC4400CWs, ES44DCs and ES44ACs. I think CN also specified rectangular windows on its Dash 9 series models and ES44s.
The oval window may have been the standard design and is what other railroads' GEs had until just a few years ago. You will see, for example that the oval window appears on the cabs of the first ES44s purchased by UP, CSX KCS and others. Those other roads in more recent years have purchased the engines with the rectangular window and thus have models with both designs. I suspect that the rectangular window has now become standard rather than a road-specific variation. Perhaps someone who knows for sure can chime in. (GE also has changed the front cab door location on ES44 models from the conductor's to the engineer's side).
So to know what is correct for a model, one has to check a prototype photo for the particular engine. Hope this helps.
RM