This is definitely something I'd like to do as well, but I wanted to focus on the areas I found problematic first and foremost. I may post a follow-up based on the feedback I've received.
> Why not have the presentation be the specification, and we can just build the html to conform to the that specification instead
As I said, I don't believe this is an appropriate approach for a medium which has no absolute, definitive interpretation. A website isn't how it looks, because how it looks will differ depending on how you access it. The only absolute truth when talking about websites is the semantic purpose of the markup underlying it, because purpose is universal: a navigation element is a navigation element regardless of whether it's being displayed on a TV, a desktop browser, a smartphone, or being read out by a screen reader.
> I imagine that's just because you'd rather see better looking html than you would see better looking css.
I'm actually interested in both :)
> You have the semantic issues well thought out, however you are flat out declaring data semantics are more important than presentation semantics.
What are ‘presentation semantics’? I think this is a corruption of the concept of semantics. Semantics are what a thing is, or means, or does; not how it is presented
> My CTO and designer (2 people I have a lot of respect for) were the people who eventually changed my mind on this. They said, "I don't know why this button is blue, but it's supposed to be green". Well it turns out it's blue because it has the class blue on it. Instead of trying to figure out what selector was causing this button to be blue, all I had to do was remove the blue class and add the green class. It took 15 seconds.
Changing how you structure the CSS in your application based on the whims of people whose area of expertise isn't CSS sounds like a nightmare scenario to me. If you're bootstrapping with a small team I can understand wanting to have everyone being able to contribute, but you should also be able to recognise what the limitations of their skills are. In the example you give, I would be using my web developer tools / inspector etc. to find out the origin of the erroneous property. If you're using a preprocessor there are source maps that can help with identifying how a rule was built. I certainly wouldn't conclude it's easier to use a presentational class name just so that my CTO could understand the code.