What the hell is the stuff in the little glass jars they’re drinking?
And the goats? What in the hell is with the goats?

No idea what they're drinking. The goats fit in somehow to the psuedo-religion Lumon seems to be all about with its founder Kier Eagan. At least that's my take.

After Dylan refused to let his “innie” resign, it became clear that that the innies were slaves.

Same with Helena and Helly. It appears the point of innies is to remove all pain and drudgery from the lives of outies, but at the expense of innies living a nightmare.

So they’re mining the data to collect all of Gemma’s “tempers”, effectively digitalizing her soul. What are they going to do with it?

Gemma was severered into 24 different innies. Her outie was trapped on the lower level. Apparently Cold Harbor was supposed to be the last but what they were going to do with her at that point is unclear since Mark's innie broke her out before whatever was supposed to happen happened. My best guess is Jame Eagan was going to benefit somehow since he was on hand waiting for whatever to happen.

What was Lumen producing in the small fishing village? Ms. Cobel and the dude recalled their time working around the vats. And why was everyone huffing ether?

Yet another mystery? The courtship of Kier Eagan and Imogene began at the ether factory. Not sure what else there is to that subplot of the storyline.

It turned out Cobel was the designer of Severance. The idea was taken away from her, but she got the plans back. Is she planning on taking Lumon down, or taking it over?

Harmony's character arc seems to have turned hard against Lumon, but she is a complicated character and who knows what's next for her? I also thought after S2E9 that Milchick was going to turn against Lumon but that didn't happen in E10.

The ending. Was Mark S. selfish in staying with Helly R.? He saved Gemma, but didn’t he owe anything else to his outie. Will both Mark S. and his outie perish? Or will we see them re-integrate. Guess will have to wait till season 3.

Keep in mind Mark has had the implant in his brain messed with by Reghabi, so who knows what his innie will do with him staying in there. Lumon would have no need for him if Cold Harbor had been a success but with Gemma's escape (apparently? She didn't actually leave the building yet) Lumon will likely want to use him further.

Irv's story will likely be explained in season 3, but my take is he is an investigative reporter (the phone booth calls, the notes and drawings) and somehow he was involved with Lumon longer than the rest.

Helly I have a bad vibe about. I'm never sure when she's actually her innie or her outie pretending to be her innie.

Dylan's innie character has now had two major revolts against Lumon while his outie is a weakling. Interesting to see where that is going.

I have no idea what Huang's character was all about? No telling who Burt really is in all this but he appears to be a Lumon insider. Mark's sister Devon and brother-in-law Ricken could also either or both be Lumon insiders. The creepy AF Dr Mauer will likely now take Drummond's role in the organization. Sandra Bernhard's evil character Cecily was an interesting add to an already excellent cast. Natalie is the liaison to Lumon's mysterious Board who we have never seen, which is another mystery. And so is the weird room where Drummond and Mauer were watching the team work with characters who resembled the team sitting at terminals. WTF was that?

So yeah, while season 2 finally answered some questions, there are way more left unanswered.