My guess is that the 15 m line was chosen because it is the least multiple of 5 m that will not force most swimmers to surface unnaturally early after the start. Had they picked 10 m, half of us would break the rule by just doing what used to be normal. Of course, by introducing the rule they also made most of us strive to reach further than before. A 50 back or 50 fly in short course is not much swimming anymore. And the same swimmer can excel in both events by just having a great kick in a way you just couldn't in the days when swimmers swam more in these events.
As for why freestyle is not free to be done totally submerged, it basically goes back to the origins of the sport. It was always done on the surface (sub-surface swimming, with mono fins and snorkels for example, is governed by a different organisation) and when flip turns were invented, no one thought about restricting the under water part of the turn because everyone returned to the surface soon enough to breathe anyway. The backstroke events at the Seoul olympics changed that. And when the rule was introduced for backstroke, it was also introduced for butterfly and freestyle to avoid the same thing happening there.
As an aside, backstroke is pretty much as free as freestyle. You just cannot chose to swim it on your stomach like you can in freestyle.