As I wrote: When you select a pixel clock (how many unique transitions) in a specific timing (border end, start) vs number of scanlines - to fit in a specific physical format (4:3) you have defined a pixel aspect ratio.
It's completely irrelevant that you _could_ make manual changes on your monitor. The above is what was define in the hardware. Any changes after the signal gets sent to the monitor is more along the lines of "monitor emulation".
This is the reason why I sourced comments from graphics artists who used to work on the platform. It's also the reason why other emulators on other platforms with non-square pixels have settings for it.
/Troed