At least for Fallout 4, it is possible to load a non-master (or presumably a master) in the FE index while light masters are also present, so they end up sharing FE at runtime. In this case, if two records have the same runtime FormID, then the non-ESL record replaces the ESL record.
This behaviour is undesirable, and may lead to strange issues due to records being silently replaced by records that may be completely unrelated. libloadorder should probably disallow activating a normal plugin in the FE slot when light masters are also present.