Not an expert but I would think not putting a board in is way easier than putting in a different one. It's also harder to manage supply for two different boards with different connectors, making different cables, split the accessories ecosystem etc.
Apple, esp. under Tim Cook, is super efficient when it comes to this stuff.
True, but that sounds like a PR nightmare. In that case I would expect them to go no-ports worldwide and claim that their amazing MagSafe charging is superior and how bold they are.
Don't forget Apple's Lightning patents run out soon.
I think rather than ride it alone in the carnage of out-of-spec Lightning kit that would undoubtedly flood the market, getting switched to USB-C (while the customers blame regulators for having to buy new accessories) is probably better for Apple.
You really think Apple applied for a patent for Lightning in 2002? 5 years before the first iPhone and 10 years before the first iPhone that had Lightning?