I have a new proposal, and way too much time on my hands. Well, at least this is more restrained than my previous few efforts. Anyway, most of the new feature stuff I'm about to ask for can be ignored. I know it's just me asking for things beyond my station, so to speak. These designs will work perfectly well without that stuff.
So, I took a look at the cargo bay on the new station, and I realized something that should have occurred to me much sooner. The inventory bars take up the bottom two lines of your view. Being on the south side of the station, that makes it a lot harder to look out and see if crates have gotten backed up, either coming in or going out, which is very important to be able to do if you want to run things efficiently. That's why I reduced the width of that buy/sell belt room from five to three. That way, you'll just be able to see the outside of the buy belt from within the cargo bay if you close your top inventory bar.
Of course, at least on that end it wouldn't be needed if it were possible to have those IR detectors I added, wired to the blast doors to force them to always be open if there's a crate sitting on the belt.
Inside the cargo bay, I've opted for an arrangement that has less open space than the current Cogmap 2 arrangement, but still has plenty of room to store crates where they won't be in the way. The manufacturers in the middle are arranged like that so you can unload the recycler into any of them. You may say that communal mode makes that unnecessary, but there are occasions where you want to leave it off so you can sell lots of recycled ore quickly. That's a pretty minor concern, though. It's a little cramped in the front, but that's to encourage the use of the front belts. Those are less secure than the front belts on the current map, but with the button to seal them right there by the ordering console, it should be secure enough. It's also the only belt with a lever to control its direction, since it's the only belt where you'd have a reason to reverse it.
Also added to the cargo bay are a general alert computer, an auto-loom and fabricator which should reasonably have a fairly broad selection of item types, and a pipe dispenser next to those, because why not? There's also a second, different barcode computer, the one with green buttons. That's so the barcodes that contain banking information can be separated from the ones that control belt destinations or selling to merchants. I believe I've expounded before on how it can be inconvenient. Once any ID has been scanned, it will always be added, so if you want to sell to a merchant without embezzling half the profits, you can't. These green barcode computers should be spread throughout the station, to make it easier for everyone (mostly botanists and perhaps miners) to profit off of selling their wares. The computer simply stores and displays a list of scanned cards, from which you can select one to print. Should be simple enough to do, just split the code out from the current barcode computers. Another ease-of-life measure would be to have "Sell" barcodes that send the crate straight out without needing to trouble the QMs. Of course, they can still grab the crates off the belt if they want to.
And then there's the disposal site off to the right. It's a lot smaller than the current one, and controlled by a different department (QMs instead of janitors) which should make it both more and less effective as a murder tool. I figure, it's best for the QMs to take care of scrapping and recycling, since they have a use for scrap. There's a recycling unit right there, so you can grab the scrap off the line and add it right in. The computer is to allow programming the belts and routers. Right now, you can't build new ones, but if you could, a central control location could be useful. Otherwise, they'd have to be programmed by mechanics, and that opens up too much opportunity for them to screw with the whole system. It could work in a pretty simple way. Just give it some space GPS coordinates, and have it detect all the belts or routers there (since there can be more than one belt on a tile). Then for belts you give it a value. 0 for off, 1 for up/right, 2 for down/left. Routers would be a bit more complicated, but not too much so. And that opens up the possibility of custom routing paths, that send crates around the station indefinitely.
Now for the second part.
This is the opposite side of that corridor, directly across from the cargo bay. Basically, I turned the janitor's room on its side and moved it over to the side to make room for the warehouse (which I didn't bother filling with all the junk it has in the current station, but pretend it's all there). Basically, this is all meant to be a big production and market district that dominates the entire east half of the southern annex. You've got the cargo bay and hangar on one side of the corridor, and on the other is mechanics, a couple kiosks for people to set up shop, the warehouse (which now has its own cargo route) and the smelter.
I didn't do the four-router thing I did on the other here, since a crate that needs to go the other way can switch belts in the disposals section side. That way it gets shot across the corridor twice!

(Or I guess people could just be not-lazy and put it on the right belt manually, if they really wanted to)
That red exclamation mark should be a false wall. Inside that little area is a corpse (or sometimes a zombie, similar to how the head surgeon sometimes spawns as a cardboard box). Along with it (symbolically represented by an evidence box) should be a randomly spawned collection of "stuff." Half-empty drink bottles with various reagents in them, maybe a working ID card, maybe low-level traitor items, or any other random thing you might find in the game. Basically, a running joke that raises the question of how the guy died each round.
This is somewhat unrelated, but I think a shuttle to the diner should also be added somewhere in this area. Maybe opposite that customs office just north of the escape arm? Since, as I understand it, merchant shuttles are now going to dock at the diner station, I figure the market district wouldn't be complete without such a shuttle.
And I think the miners could also use a cargo dock of their own. You could probably attach it to the south end of their lair, maybe with a secondary dock further out at the mineral magnet gantry, since the belts would pass by there anyway. The secondary one wouldn't need its own barcode route, but just having a couple barcode computers and a place you can grab or put on crates would be enough. I'm sure the miners would appreciate being able to freely profit off their labors without having to risk the QMs stealing from them. Also, if I'm ever trying to be a big-money traitor and they aren't helping me facilitate that, I want to be able to send them a delightful gift with a 2-minute timer. It works both ways. Sending it to a dock is less obvious than to a cargo telepad.
Adding a mining dock would also give further reason to make it so the botany/catering dock receives crates from around the west side of the station instead of through the middle, which would probably take a lot longer. Then you'd remove a good chunk of the northern belt route, leaving only enough for a public cargo dock on the south side of the corridor outside the chapel.