The "exception" doesn't appear to be the case anymore - the rep gains are only shown separated if you have gained/lost the rep only on two or more sites, and if the said downvote is removed / the votes are undone, you're back to the situation shown on your first screenshot.
I remember that if you earned rep only on one site today or yesterday, it used to show rep for this day in the way shown on your pic (also in my commentmy comment).
Exception would be if you had rep changes on multiple sites, e.g.: on MSE you had some upvotes, on SO casted a downvote on answer and then your downvote on SO is removed, you'll see your rep on this day "site-by-site", like this (I downvoted and undownvoted an answer):