No, this is not water resistant.
Yes, they just need painted. Look at Miratec, has a 50 year warranty, is mdf and is for outdoors.
I found the marks to be actual scratches in the finish. Maybe a rag with paint remover would desolve a little and buff out the scratches.
Yes, you can paint the moulding board with your exterior house paint.
At Home Depot you're allowed 1-2 (can't remember now) cuts per item FREE. As long as each piece is larger than 12" (their machines can't hang on to pieces smaller than 12", so finer cuts you have to do yourself. So if you buy 4ft (48") and need 47" - they can NOT cut one inch off for you, because 1<12). In general MDF is considered to be "easy" to cut even with a hand-saw. The appearance of the cut of finished MDF would not be too pretty, so you'd have to cover it up or paint it. For an 8" wide MDF, I used the smallest (5x6") brackets, but just because I expect to load it up with light stuff. Brackets MUST go into wall studs, more specifically, into the center of a stud, so that all 3 screws get inside the stud (I was off in my stud calculation, and one of the screws didn't make it into a stud, thus reducing the 200lb weight capacity of the shelf). You don't want brackets on outer edges anyway - too much overhang. Just try to make reasonable widest-possible setting of brackets that your wall studs will allow you.