The merge box style is intentional, it's how GitHub aligns the icons and buttons in boxes. See for example the circle on the left, also top-left aligned rather than centered

For the PR header, sure 👍

it's how GitHub aligns the icons and buttons in boxes

The merge button is centered. Icons are a different thing

For the PR header, sure 👍

I don't see the difference. It’s all just a lack of care rather than some inexplicable "intention"

I mean that same box, look at the green and gray circles on the left. Also the general alert boxes have the same style. This lets the box contents grow while placing the CTAs in the top-right

Apparently some people like their buttons misaligned. Can't argue with that

They are aligned, just not to what you're thinking. See for example the same style in the app. Vertically centering them in taller and taller boxes make less and less sense

Icons are a different thing

taller and taller boxes

Taller and taller boxes in question (77px):

Those boxes are as tall as a corgi

https://github.com/refined-github/refined-github/settings/#discussions-feature-desc