Per tzfile.5, which describes the file format, under "Interoperability considerations":

"Other than version 1, writers should generate the lowest version number needed by a file's data.  For example, a writer should generate a version 4 file only if its leap second table either expires or is truncated at the start.  Likewise, a writer not generating a version 4 file should generate a version 3 file only if TZ string extensions are necessary to accurately model transition times."

In short, this is done intentionally to maximize backwards compatibility.