The same as the very pale blue mark in Glyphs 3: it’s the insertion point in the text.
No, not the cursor point mark, the other rectangles above the D, N and T?
Those are the visualization of the kerning values. They are blue (negative) or yellow (positive). But the position and size is not what I would expect.
Are they placed above or below the pairs? I agree, what I see makes no sense to me and is distracting. Can I turn them off?
They are places below the first line. There is a bug with the positioning. I fixed it yesterday.