Might I suggest you add to section 9 in the FAQ (titled How do I transfer tag information from one tag format to the other?)
...Please remember that if you keep both APE and ID tags, some music applications will give preference to the APE tags over the ID tags, and some applications will do the inverse.
For instance, if you have a file with the tags
APE: title "apple"
ID: title "banana"
Some player applications will show the title as "apple", and others will show it as "banana".
There is no standardization in this area, so it's impossible for MP3Tag to show you which tag is going to take precedence.
The easiest thing is to only have one kind of tag or the other.