They ship the phones with a small adapter that goes from micro USB to lightning. You're allowed a proprietary port into the phone as long as you provide the adapter for free.
Except for the fact that people have torn down their electronics accessories and found them to be significantly higher quality than the crappy ones you can buy for $5.
Better components, better design, better safety,
and better assembly. Plus then you have to package and ship the things.
People complain about Apple selling $20 accessories, then turn around and complain about working conditions in Apple's suppliers like Foxconn (despite Apple doing far better on that front than their competitors).
That link's about power supplies, where there actually is a significant difference in component quality. A lightning to microusb adapter doesn't involve voltage shifting or anything else that's super problematic. About all the lightning connector does is introduce lock-in.
