Author here.

> Did Github ever solicit feedback from the community for this feature? Was there ever a beta before they rolled it out?

There actually was a closed preview for this, but it wasn't long and the feedback I gave them (which is almost everything that's in the blog post) wasn't implemented.

> The visual font size problem seems particularly disastrous:

They made the decision to match the capital heights of the two fonts, not the x-heights. If they match the x-heights, the capitals in math mode will be too large.

Since the small letters are way to small, perhaps they'll increase math font size a little bit in the future to balance it out.