my humble thoughts on this mod.
I did the deck plate mod and drove around with it open for about a week, on and off road, and for me, the only difference I could tell was noise.
I put it back on and had not taken it off in over 2 years.
That said , looking at the design of the air intake in the fender well,,I do think that can be a bottle neck. That said the deck plate mod should be helpful......shouldn't it .

I could be wrong about not feeling any gains and its there if I ever want to try again. Also last winter my fenders were so packed with snow, made me wonder if it is breathing good in that condition ? Maybe I should have opened the deck plate and seen for my self, maybe this winter

However, I do think I felt a difference with resonator box delete, big O gasket, maf and throttle body cleaning and a borla exhaust. ( done months before the deck plate mod)

I don't think you have any worry about rain - check the front of the airbox for any evidence of water hitting it.... And as long as the water isn't getting above the bumper (fording) you probably won't get water in there driving through streams, etc. It is only a couple inches lower than the fender intake.

I go back and forth on having the cover in place just based on how much noise I want at the time.

-Charlie

Phew! I am still a little sensitive to the rainy days right now because I also have a leak coming from the sunroof near the front. I noticed it when I was packing some things in the back and I was parked downhill. It started raining and I noticed water dripping into my cup holder. I did not see it when I parked the opposite direction (uphill) later that day. I also noticed that if I park with one side of the tires on the curb it doesn't occur. Neighbors think I'm crazy and they are mostly right

I have had mine installed for years. Easy mod, does it help? Maybe. At this point, my 4runner is a toy to me so i run it. I did fail smog on a visual, so keep that in mind, thanks smog guy....