OK well the fact that it hangs from the top doesn't tell us anything then. It's got extension hoses and might be hanging low enough to actually be right at the bottom.
No, it doesn't. I've replaced many fuel pumps before and they are all basically the same design. I'd say the average in-tank fuel pump is no more than 8 or 9 inches long, which is hanging from the very top of the tank. Only the pick-up (which is not part of the pump that needs to be cooled) reaches the bottom of the tank.
What??? Splashing aside, a shallow tank would be bad for cooling as it would require more fuel than a tall skinny tank to submerge the pump.
Unfortunately, most modern vehicles have to package their fuel tanks within the space available, which pretty much dictates the shape of the fuel tank. The result is never a tall, skinny tank. They are usually fairly shallow and wide, with an odd shape to them.
I have a feeling this "fact" is a lot like the NiCad scare that convinced people they have to completely discharge their battery packs every time or they'll suffer from the dreaded memory syndrome. There's some truth to it, but it's not gospel.
You can choose to believe whatever you wish, but doesn't it make sense that an electic pump will benefit from a cooler environment? I'm not saying that a fuel pump will fail in a year because of driving with a low fuel level all the time, I'm simply saying that evidence supports the idea that the cooling of a fuel pump can prolong its life. Logic is on my side, here....
If driving with low fuel is so bad, why doesn't the owner's manual advise against this? What purpose do you suppose the subtank serves?
Does the owner's manual advise against anything and everything bad? I don't think so.... I wouldn't think of the owner's manual as the only thing you should follow to care for any vehicle.
The "subtank" as you call it, is simply reserve fuel supply for those who cannot or will not fill the tank in a timely manner. In other words, if you find yourself running low of fuel (according to the fuel gauge) it will provide you with a small reserve to avoid running out of fuel completely.
Do you think manufacturers put this reserve there to use it all the time? If so, you should drive your 4Runner well past E and get every last drop out of your tank.
Personally, I would hope not to have to use the fuel reserve. But in the event that I did, I'd sure be glad it was there. Sorta like my spare tire, if you know what I mean....