Comparing to the “Many” side will produce no results because Toolset cannot know which of the many items you want to compare to.
So you cannot insert the condition and specify the relationship, the GUI doesn't let you.
But... I managed to trick it into working by using a different format for testing the Types field. Normally this is inserted as "$(wpcf-my-field)", which will evaluate my-field for the current post.
But you can also provide a full Types shortcode inside single quotes, like this:
if="( '[types field='harmfull_duration' format='FIELD_VALUE' item='@skill-harmfull-effect.intermediary'][/types]' ne '' "
So it is testing the output of the shortcode itself.