I’m trying to find an answer to this myself, it’s disappointing that I can’t use the latest FastLED features on the Photon, but I completely understand why you don’t want to manage two code bases when one should do.
Back in October:
From last week - looks like this isn’t supported yet:
The library example repo has a V2 branch, but hasn’t been updated since September:
https://github.com/spark/uber-library-example/tree/feature/libraries-v2
It’s using a library.properties file like Arduino libraries, but doesn’t specifically mention nested folders in the README. Fingers crossed that they release this soon, and include nested folder support.