The difference is that in MN the ID numbers just have one level (MN 1, MN 123, etc.). In Udana and Sutta Nipata, etc., the numbers have two levels (Ud 1.1, Ud 3.7, Snp 2.8 …_).
In texts such as the Udana and Sutta Nipata, the number in the sidebar represents the first level in the sutta ID. This may be a vagga, a nipata, or a samyutta, etc.
So for example, in the Udana, the first chapter Bodhi Vagga has ten suttas, with ID numbers 1.1, 1.2, 1.3 … 1.10. Just by saying “1.” you know that any sutta in this book that has an ID starting with one must be in there.
If we were to represent all the numbers in the sidebar, we would have to say:
1.1–1.10 Bodhi Vagga.
That does not give us any more useful information. And it comes at a cost: more complexity, more calculations, longer to read and parse the information, and more cases where the titles end up being overlong.