I can't find the option to "Create bins based on subfolders" in the new Source Browser or in Link settings in 8.6.1. (It was formerly in AMA or Link settings I believe.)
I've just moved up from 7.x so I don't know if it's gone or for how long, or if it's just been relocated? I seem to remember seeing it in 8.4.x.
This feature is obviously a HUGE timesaver when linking to many cards of media that have already been organized at the Explorer level and when starting a new project. If it's gone it needs to come back!