I noticed that as well, but only looked into it briefly.
At a glance, it appeared to be a mechanic of the <pre> element itself, and likely has to do with the history of how HTML evolved. I’ve only checked Chrome / Windows, it may or may not occur on other browser platforms.
It’s weird, and of course we want to be able to specify both padding and margin independently on code blocks, so if this is an HTML spec oddity I’m guessing Webflow would need to wrap the <pre> in a <div>, to fix this… which complicates API imports, etc. etc…
You may need to do that with Javascript and custom CSS if you’re determined to resolve it.