For now all subfolder from a parent folder are indexed. The only way to exclude a subfolder is to add it as Favorite and uncheck it to remove its content from Infuse.
Perhaps a new way would be great to exclude a folder content?
Btw, the Recently Added section is not available on Apple TV app… is that normal?
Have you tried long pressing on the folder you want excluded and selecting “Use Local Metadata”?
Have you checked in Settings > Up Next List and make sure that it’s set for either “On” or "Recently Added Only? or if your talking about the lists at the bottom of the home screen you need to make sure you have either the TV or the Movie sorts in the Library stared for those by long pressing on the Recently Added in the Library and choosing the option you want.