I've just seen the movie and may have missed the explanation, but why did Mark remove the roof from the Rover towards the end, before he tries going to Ares 4 landing site ?
This is a vestigial element from the book. In the books, there are 2 working rovers, and he hooks them up together. In the second rover, which is acting as a trailer, he needs to store a bunch of large equipment from the hab that will sustain life support (specifically heat and air). To fit the equipment in the rover, he removes a portion of a wall, and integrates the equipment into the rover and seals it up using some of the material from a pop tent (a piece of equipment in the books).
In the film, this sequence is not present. But they include the section of him removing a chunk of the rover's wall and roof and patching it up.
From Chapter 20 of the book:
LOG ENTRY: SOL 376
I’m finally done with the rover modifications!
The tricky part was figuring out how to maintain life support. Everything else was just work. A lot of work.
I haven’t been good at keeping the log up to date, so here’s a recap:
First I had to finish drilling holes with the Pathfinder-murderin’ drill. Then I chiseled out a billion little chunks between the holes. Okay, it was 759 but it felt like a billion.
Then I had one big hole in the trailer. I filed down the edges to keep them from being too sharp.
Remember the pop-tents? I cut the bottom out of one and the remaining canvas was the right size and shape. I used seal-strips to attach it to the inside of the trailer. After pressurizing and sealing up leaks as I found them, I had a nice big balloon bulging out of the trailer. The pressurized area is easily big enough to fit the oxygenator and atmospheric regulator.
In the book he removes sections of the roof to accommodate the extra equipment for the longer trip:
Log Entry: Sol 207
I stowed the panels on the roof. The trailer gives me room to store another seven (half of its roof will be missing because of the hole I'm cutting in it).
Mark was modifying the rover so that it can better handle the long distance travel. There's a montage where he is trying to get the rover ready by putting in extra equipment for fresh water and air recycling.