The things is, I've just never had those problems you mention in the 7 apps I've shipped, and I always use .xibs. Some apps of mine are simple, and some are fairly complex.
As a side note, I also hate, hate, hate using things like Balsamiq and other wireframing/mockup tools that you use a computer for. I'm a designer first and foremost (Art degree), and if I have to see something before beginning any coding/visual design work I'll draw it out on paper first. Most of the time though, I can keep the whole visual design process of which screens go to where and how they should look in my head. I think you're also underestimating how much visual design work has to happen, including after iterating a few times on the design, after doing your mockups. A few pixel shift here and there or bumping up/down a font-size, or even changing a gray from 65% black to 63% is fairly common. So, I just skip that mockup phase and start making the thing - iterating the design all the way through.
I think you misunderstand what I mean by "prototyping or quickly mocking up a design that is changing rapidly". It has nothing to do with achieving a pixel-perfect design, finding the perfect shade of gray, or the right font size. It has a lot more to do with quickly testing ideas and iterating, rather than committing to a design and trying to get a finished look.
Paper does work well for this, and you're free to not like Balsamiq.
As a side note, I also hate, hate, hate using things like Balsamiq and other wireframing/mockup tools that you use a computer for. I'm a designer first and foremost (Art degree), and if I have to see something before beginning any coding/visual design work I'll draw it out on paper first. Most of the time though, I can keep the whole visual design process of which screens go to where and how they should look in my head. I think you're also underestimating how much visual design work has to happen, including after iterating a few times on the design, after doing your mockups. A few pixel shift here and there or bumping up/down a font-size, or even changing a gray from 65% black to 63% is fairly common. So, I just skip that mockup phase and start making the thing - iterating the design all the way through.