What causes an entry's field to be marked as "modified" when the entry is saved?
When an Edit Entry page is loaded, Craft takes note of all the fields’ current form values, and when the form is submitted, only field values that have changed will be posted. As far as the back-end is concerned, if a field is included in the post data, then it was changed; otherwise it wasn’t.

I suspect that the modified param you are seeing is a Neo-specific thing. Sounds like maybe they have their own change tracking going on, which is separate from how Craft does it.