These "new" s4 hosts (and probably the rest too) were probably recloned from a host not using file per table and they have a huge ibdata file and a few ibd tables:
root@db1081:/srv/sqldata/commonswiki# ls -lh | grep ibd -rw-rw---- 1 mysql mysql 9.0M Mar 22 06:53 babel.ibd -rw-rw---- 1 mysql mysql 9.2G Mar 22 09:53 filearchive.ibd -rw-rw---- 1 mysql mysql 128K Mar 9 21:11 linter.ibd -rw-rw---- 1 mysql mysql 18G Mar 22 09:55 page.ibd -rw-rw---- 1 mysql mysql 106G Mar 22 09:55 revision.ibd -rw-rw---- 1 mysql mysql 112K Dec 8 23:50 securepoll_elections.ibd -rw-rw---- 1 mysql mysql 8.0M Mar 22 05:49 user_groups.ibd root@db1081:/srv/sqldata# ls -lh ibdata1 -rw-rw---- 1 mysql mysql 1.2T Mar 22 09:56 ibdata1
Servers that need to be migrated to file per table:
- db1059 (no longer in s4)
- db1084
- db1091
- db1097