Thanks for the Steam suggestion - I have the same Steam settings as you but after a bit of experimentation I am convinced that it is Steam creating this problem. As well as your suggestions, I also right-clicked on MSFS in the games list, clicked Properties, Controller and then selected "Disable Steam Input". I really felt this was going to work, however I still have the ghost controllers - but I now only have two, not three!
I believe the problem is that in the latest versions of Steam client, Steam Controller support can not be disabled completely. Indeed, in the Controller menu mentioned above, it states that Steam Controller and Remote Play are "Enabled, always required", and from a brief search online it seems impossible to change this setting.
Interestingly, the positions of the "virtual" controllers in the FSUIPC7.JoyScan.csv file seem to determine whether these controllers cause an issue or not. I still now have two phantom controllers in my list, however since they are the top two entries in the list, they do not mess up my FSUIPC7.ini [JoyNames] section.
Thanks for your help John, and no pressure at all - it's not a game-breaking issue, just a slight annoyance!