It's not just one less port, it's also that the 3.5 mm jack is pretty long so I bet it'll make the hardware design of the internals a lot easier.
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Not true, just take a look at the iPod shuffle. That tiny thing is purely a motherboard and a battery. The 3,5mm jack only takes the space physically needed for the plug to get inside, nothing more nor special design.
https://www.ifixit.com/Teardown/iPod+Shuffle+4th+Generation+Teardown/3559
If someone has a lighting cable at home please put it next to a 3,5mm jack and tell us how big is the long difference... I bet it won't enough to make all our music headphones and speakers obsolete!