MTR supports nested test suites, such as suite/engines/funcs.
It is run by providing the suite value as

--suite=engines/funcs.

Overlays do not support this. If I create storage/<engine>/mysql-test/engines/funcs and then run

perl mtr --suite=engines/funcs- 

it dies at lib/mtr_cases.pm line 383.

It seems that the change below fixes it, although I might fail to predict some deeper consequences.

@@ -380,7 +380,7 @@

     local %file_combinations = ();

     local %file_in_overlay = ();

-    die unless m@/(?:storage|plugin)/(\w+)/mysql-test/\w+$@;

+    die "Overlay not found" unless m@/(?:storage|plugin)/(\w+)/mysql-test/[\w\\\/]+$@;

     next unless defined $over and ($over eq '' or $over eq $1);

     push @cases, 

     # don't add cases that take *all* data from the parent suite

Please replace the death message with something appropriate, but it's better to say something than die quietly.