This is how I have approached sealing/preventing “most” of water + dust from getting into the rear part of the tacoma tailgate area. I used this tailgate seal found here: ESI Ultimate Tailgate Seal (Amazon)
I also used this in the past to seal the gap between my tailgate + bed of the truck but wasn’t the hugest fan of it. It was most a “dirt collector” more than anything in my experience.
For those pesky corner, using something like this Black Butyl Tape can help out a ton. This is where I find/found most of the dust coming in at. Easiest way to see spots/holes is to do this during the day, climb into the back of the bed and see where daylight is coming in at.
I found it easiest/best to pop or slightly take off my tailgate also. My bedrug covers the seal under it but I also used tailgate seal under there. No daylight came through before covering it with my bed reg.
Now, I also saw this YouTube video where he put the seal on the actual tailgate vs how the company shows it on the bed of the truck. I do believe this has also helped out a ton, especially in/near those top corners of the tailgate. I found lot of my dust/water also came in via those areas.
Along with the butyl tape, putting a small strip of the tailgate seal on the rear hatch/door so it helps with that pesky corner can also help. See the below photo as I did this on both sides.