I'm definitely one of those who treat it like a filesystem :') . I'd love to hear a different point of view. Would you feel ok to share thoughts on how I could be thinking of s3 to fully appreciate the right way of using it?
Object storage is best for larger files with bulk updates. Either write new files entirely (best for S3) or append/replace where supported (like Azure/GCP). Any further structure and metadata should be maintained at a higher level with pointers to the raw files in the object store.
There are products like Stablebit Cloud Drive [1], ObjectiveFS [2], and other storage companies that handle all this for you. You can also look UtahFS [3] to see open-source code on building something yourself.
1) https://stablebit.com/CloudDrive 2) https://objectivefs.com/ 3) https://blog.cloudflare.com/utahfs/