Here's the analysis of the before and after raw dumps which were sent:
First off both files are well formed and are not missing any of the udta-meta-ilst atoms.
The first file (before Yate) has 0 free bytes. Adding even 1 byte will cause the file to be rewritten. The second file has 2048 bytes of free space which is the Yate default and is what I would expect after writing the entire file.
The issue is that Yate writes more metadata than the other application. This is common for all audio file types. There is no way I can add in per field granularity for every field and every tagger tends to write a different set of metadata. In this case the additional items are not empty. (Empty items are not written).
Here's the detailed breakdown discussed primarily from the Yate edited file.
76 bytes were added for the Media type.
25 byte were added for the Content Advisory
24 bytes were added for the Show Description
The Show Name decreased in size by 10 bytes
72 bytes were added for the video classification.
233 bytes were added for iTunMOVI. (This can be disabled in Preferences-Audio-MPEG-4-Process iTunMOVI for files with video)
The net difference is that 440 bytes were added.
The other application more than likely does not rewrite the file as you have reduced the size of the Show Name field by 10 bytes. In Yate this is negated by the other added metadata.
There is no way to look at this situation as 'I only want what's in the other application'. The added metadata may not be useful to you but it is used by many others. Also, as I said already said I cannot build in per field exclusion.
I understand your angst but 440 bytes in a video file is insignificant. Not having any free space in a video file is somewhat insane. v6 of Yate will allow different free space allotments for audio and video files.