Based on the article, it's happening before anything gets served, it's specifically happening during the Astro build phase, but only on the Cloudflare build machines. So by the time it comes to serve the assets, stuff is already broken.

My guess would be that there is some specific bit of information set during the build that triggers this incorrect build in Astro, and this information is set only by the Cloudflare build process. But here the people from Cloudflare are struggling to reproduce that effect, so it looks very specific to this person's setup.