I have a few questions. Thinking a little outside the box here...

1. I went alone and Cooke is doing the chem deal betrayal with me.
2. I convinced Trish not to tell her boss. Does she actually tell him or not if she survives and agrees to this?
3. Cooke pulls a gun on Trish if you spare her, regardless. I pulled a gun on Cooke and killed him.

What exactly flags and what doesn't?

Does it count as me killing Cooke if he dies by my hand during the ambush or at all?
Does Trish tattle on me to anyone, as in... do I have to deal with Nelson or Marowski coming after me?

Long story short. I think it's BS that Cooke kills Trish after I get her agree to be cool. However, if I'm just asking for a can of worms of weird glitchy story and/or anything else, I'd rather just have Trish die and keep everything a clean getaway with only me knowing about the chems and profiting from it all and no loose ends hassling me days or weeks later since

1. Cooke lives.
2. Everybody dies at the shootout so nobody knows who did it.
3. Paul doesn't know jack.

EDIT:

Also, if Cooke's daughter comes to investigate his death, does Paul do anything at all if he's in the dark about it all? Will he still assume I killed Cooke if I tell him otherwise? There seems to be a lot of weird variables in this quest, so I'm trying to keep things straight.

Depending on what happens, Cooke supposedly leaves the Commonwealth and tells you to tell everyone he died. At that point I felt like he was just leaving me with this whole mess to deal with so I pulled a gun and killed him. I was worried that I may have broke the game, but after using Trish's notes (I killed her too..) and found the chem lab, the quest completed itself and after a few visits to Diamond City, I actually dealt with the consequences of my actions.

It seems things went a lot smoother with you than they did with me, so expect a visit from Nelson Latimer's father as well as Cooke's daughter.

I'm not sure if this quest is bugged. I agree to let Trish live both regardless of dialog choices, Cooke still attacks her. Reloaded a couple of times now, if I kill her I get the option to split the loot but surely if I let her live the Cooke should become hostile towards me if he is gonna kill her anyway

In my game Cooke shot Paul in the bar, and then Cooke and I went to rush the deal. I fast travelled and didn't wait for him (Didn't know he was gonna run there like that) and then destroyed the drug deal with a missile launcher before even talking to anyone. Trish survived and then tried to kill me so I shot her and then did the chem lab thing, but I never talked to Cook again and I can't get into the crates to steal the chems haha. Boo!

Yeah, he's an [censored] like that. I don't think it's a bug, it's just that Cooke plays by his own rules.

Honestly for as many variables as there are, there aren't variables or responses for the things that make sense.

1) Yell at Cooke for killing Trish when you promise to spare her (because it's a persuasion check, it could be considerered that you're lying to her... but then the "threat" check is more difficult, so really none of it makes sense.)

2) The options to talk to the dealers where everything results in a fight. You'd think there would be a double-cross option where you could tell them Cooke is trying to screw them over, and maybe that ends the quest or opens a different quest line or something.

UPDATE: I'm still making my way through this quest, but I've learned the following...

- No matter what you do to Cooke, if Paul isn't present, he will assume Cooke was killed by you.

- If Paul isn't present, and you complete the drug deal without talking to Paul, the game will treat it (in the quest description) as if you had talked Paul out of all of his cut of the chem deal. This may result in backlash in the post-quest scenarios that involve him betraying you.