With Esri support we verified that there is no way how to check following checks when need to compare feature class and M:N relationship class.
Control definition for point feature class (FC):
checkquery: whereclause="TYPE in (1,2,5)"
check expression: "RELATIONSHIP_CLASS_NAME" min="1" max="1" not="true">
check err message: "This type of point must have exactly one related feature in given relationship class"
This example says - find all point features that do not have exactly 1 record within the M:N relationship class.
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