Both of the odd aspects of the tuning you've noted are caused by the same thing: Harmonicas are originally designed to play chords! It was basically built by 19'th century Germans to play polkas.
And not necessarily just two or three notes at the time as you guessed, but possibly more! A harmonica in the key of C, as the one in your chart, was designed so that any way you could possibly blow into it produces a C major chord. When you draw, on the other hand, the entire lower half of the instrument produces a large G7 chord. This is the dominant to the C chord, and it's thus really useful when playing in the key of C. The notes DFA constitute the minor parallel of the subdominant, and you could even use the two notes FA to suggest an F major chord, the subdominant of C.
(In other terms you have the chords I, ii, (IV) and V7)
The chords are prioritised in order of importance, so that the one most important chord gets a lot of space.
The notes have been adjusted somewhat to allow for playing a melody in the upper half, but at least the bottom half is mainly intended as a chord instrument.
This doesn't mean you can't play melodies on it. In fact, people have spent over a century coming up with techniques to make the harmonica do things it wasn't intended to do. Today people are playing it fully chromatically, i.e. with all the notes you find on a piano, and some between as well! People DO play fantastic music on standard tuned harmonicas, it's just that there are quite a lot of hacks involved in their doing so.
Then, of course, no-one is forcing you to play the standard tuning if you don't like it. Though this is the most common there are many alternatives to choose from from many different brands, some tunings are even designed to play modern music ;)