Hmmm, I'll muddle through with you until someone more in-the-know comes along. The vinyl in the mystery port could indicate the liner installers were told that plumbing had been abandoned, or they might have just forgotten to do what you did. So that doesn't really tell us anything.
I don't know how to winterize a pool, so I wouldn't know if you're supposed to cap off a main drain or not. I've never heard of that, nor read about someone having to dive down into a pool each winter to swap a drain cover for a cap. Some drain covers have their openings around the perimeter, somewhat obscured, and have no slots on the top. Is it possible you're looking at something like this:
And while unlikely, I suppose you could be looking at a diverter plate under the skimmer basket, which might have a single hole in it, but actually be covering the two ports underneath it, the suction port, and the main drain port. So that's the first and easiest thing to check.
If you can find two ports in the skimmer, that usually means one to the pump, one to the drain.
If there's only one, and there is no diverter plate, then that leads to the 3-way valve, and would imply that the main drain is plumbed to the pad, to the 3-way.
With two pipes coming out of the ground into that 3-way Jandy just in front of the pump, that's likely either balancing the suction between drain and skimmer, or vacuum port and skimmer. It'd likely be the former if you have only one port in the skimmer, and the latter if there are two ports in the skimmer.
With me so far?
There are quite a few possible scenarios, but before we explore all those, you need to know for sure the number of ports in your skimmer, and whether the drain is capped off or not. As I said, you could be looking at a pool that was intentionally made safer by capping off both drain and suction port. Or either could have been capped off or abandoned because of a leak in one or both. Or maybe the suction port got hopelessly clogged and was abandoned. Maybe the drain did plumb to the skimmer, but the skimmer was replaced and the drain line abandoned at the skimmer and capped off at the drain. Lot's of possibilities.
No way to contact the previous owner, through the realtor, maybe, and ask a few questions?
Anyway, first things first: confirm number of ports in skimmer, confirm drain is capped, and not just covered.
The good news: you have a working skimmer and two working returns, and that's all you need. So you don't have to even bother with the rest if you don't want to. (Except to plug up the mystery port again and render it 100% safe.)