I think that the basic design of MP3tag will not be the best to implement this.
As you can treat more or less any tag version (wav, flac, V1, V2.3, V2.4 mp4 etc.) and any file type (ogg, flac, wav, mp3, mp4 etc.) the read data has always to be mapped to an internal representation.
If this is the case: which of your other program stacked tags on top of each other? Such a treatment of files is definitely the wrong way.
Where do you see this display?
Have you checked the extended tags dialogue to see how many fields there are?
Here are links to some utilities to check files for corruption:
AFAIK the case of a tag field name should not matter.
In a way you are right that subordinate tag data is not shown. Priority of tags when read is:
APE>V2>V1.
But you see which tag version is now the one with priority in the dialogue title of the extended tags dialogue of a single file or the corresponding column of the default shipment.
If would be intersting to see such problematic file and then find a way to deal with it with the current functions.