I don’t know Font Explorer, but from what I can see, it looks to me like Font Explorer only has a single ‘library’ with sets and subsets underneath it. You could do the same thing in Suitcase. Have a single library of fonts, and organise into as many sets as you like, including nested sets.
Libraries were added as a new feature in Suitcase Fusion 2 (v13) to enable you to keep certain fonts completely separate from other fonts. Hence why you only see the contents of a library when you select it, and don’t see the other libraries at the same time. If you go all the way back to Suitcase Fusion 1 (v12) and earlier, we didn’t have such a feature and everything was stored just in a single ‘library’ of fonts, with the ability to create nested sets as you wished. Most customers will still only have 1 library therefore in Suitcase, and manage everything under that. Perhaps you could reorganise your Suitcase along the same lines, to a single library, rather than creating separate libraries?