Upon further reflection, I think this is actually the most flexible, granular, easy, and clean approach.
To elaborate slightly, you could (optionally) place a e.g. plex.txt file within a folder you wished to apply tags/collections to.
This plex.txt could be structured something like:
# Plex metadata file
# Add each tag you wish to apply on a seperate line.
# To apply the tag to items in subfolders as well, append with "-subfolders"
Tags:
IronMan
Antman
Phase2-subfolders
# Add each tag you wish to apply on a seperate line.
# To apply the collection to items in subfolders as well, append with "-subfolders"
Collections:
MCU-subfolders
Avengers