One theory here might be that Sponsorblock isn't "getting" to run, since the main browser window isn't on YouTube.com. Can reproduce thism, and confirm it works in Firefox via embeds for me as well.
I tried manually giving the above site permission to run Sponsorblock, but it doesn't appear to attempt to invoke Sponsorblock. I suspect this might be related to per-site extension permissions or "triggers" that can invoke a plugin perhaps not considering embedded content origin, and only considering window origin.