You’re right if you want to backup just a single file your going to find a whole server backup/snapshot is not very efficient. (Just not that DigitalOcean snapshots only charge for the actual used space on the server not the full disk size), So if its a small server and your only using 3gb of data for example that would cost $0.05*3 = 15cent per backup per month.
There is not currently a DigitalOcean service for backing up data off the server, I think someone asked for this in the Idea board before and someone from DigitalOcean said they would never provide a service that required logging into the server due to there own security.
So to answer your question you have lots of options.
-> You could setup a cron script to backup your data to DigitalOcean Spaces or AWS S3
-> You could setup another server and then run CRON to scrp/rsync
-> You could use a backup service.
Full disclosure I am the founder and CEO of SnapShooter a backup provider who specialises in this sorta thing especially for DigitalOcean Customers.
We have a backup function for file backups that backs your data from your Droplet/server to any S3 storage you wish. We are totally free for one job.
Check us out Droplet File Backup Service or if you want a hand setting up one of the other options let me know we love helping people.