I don't see that there is a problem with having numerous definitions for time zones with a different TZID or TZNAME but with the same time zone information.
Time zones, by nature, are under local governmental control. If there are two or more locals at the same UTC offset, then they would fall under this case.
A given time zone may have had its definition changed over time. This would account for multiple definitions for the same time zone, also.
Likewise, the duplicate definitions could result from a change in the name or identifier of one or more of these time zone definitions.
In any case, our role is merely to capture all the definitions in a common format. Not to become time zone tsars and redefine the time zone definitions, names or whatever. Right?
-- Frank