There isn't infinite time and money in the world. Every hour making one feature more stable means an hour not invested in another. Flexibility and control are just additional features. If you want to change the system font, you have to test (and support) a much wider array of things, especially if your UI guidelines are as restrictive as Apple's. Every piece of control you expose to the user increases the engineering cost of writing and maintaining the software.
And frankly, if more people wanted that level of control, this year TRULY would be the year of linux on the desktop. But they don't.