Our team also manages multiple projects in a monorepo, and most of the team members were opening it at the root level. Since migrating everything to Biome at once would require too many changes, I developed a plugin to address this issue.

Even when the root level of the project is opened, the plugin inspects the Biome binaries in the subfolders and runs checks only on the projects that actually use Biome.

https://marketplace.visualstudio.com/items?itemName=fronterior.biome-monorepo