Posting here in case anyone at Adobe can either chime in or help fix this in future updates.
When I import a folder into my project it will create a bin with the same name as long as there are 2 or more files in the folder. If there is only 1 file then it will disregard the folder and import the 1 file with no bin. Is there a secret setting somewhere to fix it so it still creates a bin? Is there a reason for this? Can it be fixed in a future update of Premiere?
Try placing a PNG in each folder and subfolder in the Finder or Explorer prior to importing the folder and subfolders into Premiere Pro. A screenshot called "placeholder.png" should work. For cleanup, use the Find Bin Content text field to locate "placeholder", select all the PNGs listed, and then right-click to use Make Offline..., Media Files Are Deleted.