Thanks for the hint, learned a lot following down the rabbit hole of trying to disable same-origin in chromedriver. (tried passing various "chromeOptions": {"args": [] } as described at
https://peter.sh/experiments/chromium-command-line-switches/ ). Finally, I tried to replicate the problem by creating a minimal test case and looking at which headers might be causing this.
It turns out that there is no problem accessing the iframe from different origin, but instead new version of stripe checkout (iframe in question) with different element id's was served to Chrome and Firefox. D'oh! (To my defense, I was using Chromium to inspect the page, wouldn't have thought it would be treated as different than full Google Chrome...)
Cheers