I think that is most likely a lot of what drives that divide, but this almost certainly the case for the port. Some shit undoubtedly is software locked, and that is in fact scummy, but new hardware will always be more expensive than hardware you have already designed and maybe even have lying around.

To get thunderbolt in there they probably need a new board specifically for the iphone, while they can just cram in the lightning version with a new solder job and call it a day.

At the end of the day 95+% of the people who will use their phones will only use the port for charging anyway.