I am not entirely clear if you are making your own shelves or not, but it sounds like you are not buying the shelves and brackets as a combo.
In both cases, do not underestimate the task of drilling the holes in the shelves to accept the rods. The holes must be perpendicular to the surface (in this case the edge of the shelves). Typically we use a drill press to make perpendicular holes, but it won't work for a hole this big and this deep. I hope you have figured out this part. If the holes are not perpendicular your shelves will be leaning up or down.
The mortise to accept the rectangular part of the rod can be easily done with a chisel or a router.
That being said, I think the first option is a bit easier to install. All you need to do is have them correctly spaced out and level. The rectangular plates ensure your rod will be perpendicular to the wall. However, for the 2nd option, you need to drill the holes and ensure they are perpendicular to the wall. Not a problem since it's drywall and you can make adjustments, but make sure you don't hit place your rod where the studs are. Just more planning and tweaking.
If you can make perfect holes in the shelves, attaching the rods to the walls should be piece of cake with whichever option you choose.