The WordPress Foundation and Automattic Inc are two entirely separate entities.
You are right in saying that they share a nearly identical relationship - however this small difference is extremely key to the difference in the overall philosophies of the platforms, in my opinion.
First of all, gorgeous mockups! I love where you're headed with the design and user experience. The cluttered WordPress dashboard and clunky post editor are my least favorite aspects of WordPress. I also really like how you're incorporating Markdown syntax.
There are a few points where I disagree.
Forking WordPress would mean keeping loads of legacy code. It would also mean you'd be binding a future platform for publishing to technologies WordPress adopted nearly a decade ago. Why use PHP? Perhaps Python, Ruby or server-side JavaScript (Node.js) are better choices. Why use MySQL? MongoDB or PostgreSQL may be a better fit.
Wouldn't merging 8+ configurable plugins into core be contradictory to avoiding bloat? Shouldn't you start with a clean slate? The plugin system is a great way to customize your environment to fit your individual needs. If you add defaults, you make it less personalized. You also add more bloat by adding functionality not everyone wants.