A lot of those design decisions can be explained by Apple’s push towards smaller, more waterproof and more durable devices. Like you mention, these choices do make Apple money. But, they also lead to a superior product.
As for waterproofing, the Samsung Galaxy S5 proved that you can have both a removable battery/SD card and maintain waterproofing. Plenty of action cameras have removable batteries too that don't compromise waterproofing.