After painstakingly finding the related issues, I finally found them:

There's a discussion for UnoCSS here: https://github.com/unocss/unocss/discussions/4604

Which linked to an issue in Tailwind here: https://github.com/tailwindlabs/tailwindcss/issues/15005

Tailwind v4 uses @property to define defaults for custom properties. At the moment, shadow roots do not support @property. It used to be explicitly denied in the spec, but it looks like there's talk on adding it: w3c/css-houdini-drafts#1085

There are a few workarounds shown in the issues.

For me, I guess I'll just manually add the preflight-only style globally. 🫤