John,
Your post, whilst well thought out, is what I think is another problem with over regulation in GA. Are you saying that if I have an STC for a modified passenger door, then the aircraft is no longer 'bog standard' and that any other STC for any other after market modification, no matter to what systems it applies to, no longer applies?
Have I read your comments correctly?
So, my door mod renders my aircraft non-standard, and therefore I must get an EO for my transponder, rather than use the STC? That is what I understand you to be saying?