We have multiple versions of fonts available in our environment (Type1, TT, and access to TypeKit) so having the ability to indicate specific fonts as "Mandatory use from Adobe Fonts/Typekit" would be helpful. In essence, the user wouldn't have to manually activate/deactivate to achieve the correct combination of fonts.
For example, the user may have Proxima Nova family Type 1 active, but the document correctly shows the TypeKit fonts as missing. They then activate their TT family, which also fails. They tend to not think of Typekit as it's not searchable in our font management tool.
Using the Document Fonts folder can help in this arena, but it won't help with AdobeFonts/Typekit fonts, and other issues creep in.
Font mangers, like Extensis Suitcase and FontAgent, don't seem to consistently recognize the availability of an Adobe Font/TypeKit font.