MySQL DBs taking up way too much disk space
I solved this issue by setting innodb_file_per_table = 0 in my MySQL config (/etc/mysql/mysql.conf.d/mysqld.cnf) and re-importing the mysqldump after dropping all databases. The ibdata1 file that contains all DB data is just about 2.4 GB.

root@ip-x-x-x-x:/var/lib/mysql# du -sm * | sort -nr | head -15
2445    ibdata1
48  ib_logfile1
48  ib_logfile0
12  ibtmp1
11  dbvwgcayak57wx
11  dbmuj7j8scnzt6
11  dbmmqtf5sss9pk
11  dbf9ynyscjzw83
11  dbdr5hk7kvsh73
11  db3mj8b7b5ezuw
11  db22z4jcfbf9yn
4   db7b5ezuwb8ca4
1   phpmyadmin
1   mysql
1   ib_buffer_pool


Seems like having a *.ibd file for every single table can actually be disadvantageous if your DB contains a lot of small tables.