I think you're right that it was used as the pickup, but what I meant to say is it would be better to use that as a drain because that location would end up sucking up all the crap at the bottom of the tank whereas the pickup tubes are usually suspended above the bottom.
The usefulness of an aux tank is debatable. Personally, it's my favorite mod on my 40, I never have to worry about carrying gas cans again. For others it's a waste of money or dead weight. But if it's something you already have and you've got nothing else taking up that space, I don't see much downside. Worse case you just keep it empty until you need it.
I don't know if the any of the aftermarket tanks are coated internally. When I cut a spot for the fuel sender in mine and I don't remember it having a coating. I thought about putting one in but I figure if it lasted 30+ years without one, I probably don't have much to worry about. Since it's already out of the truck a can of sealant would fix most problems.