First photo: yes. You can omit it if you want. If you want a screw there, use one with the appropriate grommet behind it. All three of those holes should have grommets in them; they will be covered by the mudflap and/or running board endcap (which you apparently don't have). I'd use the short self tapping screw, 90159-60182, and the 90189-06005 grommet, in all three positions, if I didn't have mudflaps or running boards. FWIW, there is a mudflap for trucks which didn't get running boards, 76604-60011 & 76604-60021. I have them on my trucks which don't have running boards; they keep road trash off the rocker panels and lower door edges.
The two screw holes in the lower rear edge of the fender fasten the fender to the body. There are weldnuts inside the body to which they are connected.
If you remove the plastic interior panel at your feet, and pull the two wiring harness connectors out of the pocket behind it, you'll see the sunroof drain hose in there. That pocket fills with water until it can run into the rocker panel under the doors and then discharge out of the pinchweld drains in the rocker panel.
The best way to prevent water from pooling in that pocket, which should never have been used for that, is to remove one of the two lowest mounting bolts. This way, water can only pool up to the height of the thickness of the weldnut, before draining directly out of the body panel. It never makes it into the rocker panel, and, as a result, your rocker panels stay dry and don't rust out.
A better solution is to do with the front drains what Toyota did with the rear drains: make them long enough to exit THROUGH the body and drain into free air. Look under the rear fenderwell and you'll see what I'm talking about. The rear drain hoses are long enough to do this. Why Toyota didn't use the same length hose in all four positions and run them out of the body the same way is beyond me.
To do this (which I have done) you need to drill a large enough hole in the fender to admit the drain hose. The grommet the rear hose uses is NLA, but the 100 series drain hose grommet, 90480-26014, is still available, or was yesterday. The 80 series rear drain hoses are NLA, but the 100 series, which are the same size, are still in US stock: 63249-60172 (RH), 63249-60182 (LH).
You do not need both bolts, however, if you want to have two bolts there, as Toyota intended, you need 90119-06420. You will also need to religiously clean your rocker panel pinchweld drains, if you install two bolts in the lower rear fender position. If they become blocked, the water will back up in the body panel pocket behind the plastic trim panel, and either (a) oveflow onto the floor under the carpet, or (b) cause the sunroof drain to fail and water will spill out of the sunroof tray onto your lap, or, if you're lucky, down the A-pillar and under the carpet, or (c) both.
IMO, you do not need both bolts because there is another bolt 90° away from those two, on the firewall, under the inner fender, about 4 inches from them. It's hidden, unless you remove the inner fender.
HTH
