The problem comes from "WL#8159 Include Sys Schema in MySQL 5.7"
(commit 498aa96e33d4a3e9b08d9f5f20288ff35a1a050f) which adds a new
(system) table outside of the mysql/ directory in the sys/ directory.
But innochecksum_3.test assumes that $ENV{MYSQLD_DATADIR}/mysql/*.ibd
will match all InnoDB tables.

Thanks to Leith, satya and marko for helping me nail this down.

(cherry picked from commit a30df797e3cb32761e05cd6b4ccd6d81c59ec0b8)