I have a feeling were it up to the people leading the project, the init code would be made available. However Intel as a company is only going to take so much risk in support of this experiment. I have a feeling that init code and firmware for softloaded peripherals will be "business as usual" for quite a while.
That said, the squeaky wheel gets the grease. If this is successful and if customers are very vocal about not wanting "half-assed" open systems, it might eventually get there.
1: Actually, in terms of resources I'm sure it's tiny. In terms of culture on the other hand...
Since Intel wants everyone to use their code (preferably in binary form), I'm not sure how useful the BIOS Writer's Guide still is. Probably just a guide on how to integrate their code into whatever you're doing yourself.
Let's see if an Intel group manages to coerce the chipset group to release those "precious" (but in reality, very boring) details on memory initialization to the world.
So far I'm doubtful, even if it's "just" for Atom.
[edit: In fact, their website (http://www.minnowboard.org/technical-features/) states "All software will be provided in image and Open Source form (with binary elements per IP restrictions)". That exception _will_ cover Platform Initialization code...]