I doubt it's an intentional thing that Apple has just decided to do, but a technical limitation of their obsession with size / thinness
the larger iPhone provides more internal space for additional features that they apparently are unable to provide in the smaller model. Much of this is because of the old Apple joke of "thinness"
you can see that a lot of Android competitors have decided that thinness isn't the only key factor anymore, and 1 or 2mm of extra girth, to keep all functionality available is a trade off a lot of people are worried about.
Look at the transition from S6 to S7. Biggest complaints of the S6 was Battery life, lack of SD card and protruding camera bulge. So instead of doubling down on thin, they thickened the chassis a couple MM, increased battery size, put the SD card in, and made the buldge smaller for the camera. At the end of the day, nobody cared that the phone was 2mm thicker. They cared that they had improved battery life, an SD card and better looking phone without as much a bulge.
Eventually though, Even Apple is going to hit a point of time where their super thin goals are going to interfere with being able to provide things that people want in their phones.