I'd like to point out that the 1FZ-FE is poorly designed. I don't particularly care for the design of it. The plugs and wires take 30 minutes (with two step 6s) to change. The concept of having the plugs recessed in where you need an actual 16mm plug socket to remove them is ridiculous.
Let's be fair, though - the truck was originally delivered with a good spark plug wrench in the tool kit. It was the least of my issues with my spark plug job. A joy to use. Getting the old wires out of the wells - that was a pain. Some of them were stuck pretty good.
The recess is due to how close the cams are and the need to optimally position the spark. It's pretty common on modern inline engines. Easier to deal with on coil-on-plug engines because you have something solid to yank on rather than just a rubber boot.