Just want to be clear on what's up here...
In the first pic I've added here (modded from yours), I think I see the ball-type scupper you've added (green arrow), correct? And you say that it is fed from a drain hole (flat, I guess?) on the deck. Is there a hose or somesuch between the deck drain and this scupper?
You say that this ball-type scupper is below the waterline, right? (I think the ball type specifically says "not for below waterline"). Perhaps more important, is your DECK (at the drain hole, anyway) below waterline? (Whether at rest or when people move to the stern)
Did you add this deck drain (and/or the exit hole the scupper itself covers), or was it there already? If there already, does it look factory, or did someone else do it?
I see a livewell intake with screen over it and your garboard drain...what is the other thing? (orange arrow)
In the second pic (also modded from yours), what is this thing on the transom (red arrow)? Is it a scupper? Is there another on the starboard side of the transom? Do these go below waterline with weight / people shifted to the rear? If they are scuppers, how "tight to the deck" are they? Also if they are scuppers (or even if they're not!) does any water come in through these? Do they have one-way flaps inside? Did you install these, or are they OEM?
Also I think someone asked (but you haven't answered), is there a place to put a bilge pump? Is there an actual bilge space under your deck? Or is the deck basically "the bottom of the hull?"
It looks to me like your transom does have something of a splashwell to it...do you get significant water over your transom and onto the deck?
I'm asking all these questions because I'm beginning to suspect that what happened is that your boat (like mine) suffers from a little water intrusion through the scuppers (and maybe over the transom--in my case the notch for the outboard is the worst culprit by far!), and someone (maybe you, maybe a previous owner-maybe even a dealer or the factory!) tried to fix that with a deck drain...except that this cure turned out to be worse than the disease, because the deck is so low that the water just pushes it's way back in the drain!
I'm learning that this "wet deck" issue is pretty common in 17-18' "bay boats" just because the decks are so low / close to the waterline.
Newer such boats (say, mid-2000's and up) appear to be addressing this with "Euro-style" transoms and/or actual splashwells. And by shifting weight (batteries, seats, consoles) forward a bit on deck, to counteract the way modern outboards have ballooned in weight versus the old days.
Cures for existing boats with this issue seem to range from "very effective but high-dollar"--like going to an outboard bracket and filling in the transom notch / raising the transom; to "medium dollar but marginally effective"--like trying to retrofit some kind of home-engineered splashwell; to "low-dollar, but learn to live with damp feet"--like having deck drain(s) that feed the under-deck bilge area and the water gets pumped out through (automatic) bilge pump(s). BTW, this is why I ask if you have under-deck bilge area, to see if deck drain to bilge is even an option for you...I'm thinking about trying this in addition to my scuppers, and/or add more scuppers--at least my deck should clear of on-taken water faster than it does now through only the two small scupper holes!
What I'm really hoping is that we can come up with something "medium-low dollar but effective," doesn't rely on crappy Chinese toy bilge pumps, and is perhaps innovative to boot!