Currently the Avro Merge strategy in MergeContent requires that any key/value pairs in the Avro non-reserved metadata must match. This might have been done to support re-merging of split Avro files upstream, since the "fragment.*" capability was added afterward.
Now that the fragment.* attributes are available to help merge a batch of flow files, the user should be able to select the Avro Metadata Strategy the same way as the Attribute Strategy, with the additional option of "Ignore if unmatched", which should be default to maintain currently functionality.