To me they are perfectly complementary. In FWWM Laura gets her happy end. We see her again in The Return and behind her face is nothing but light - she has in fact because an angel of sorts, her sins forgiven and her soul at peace.
Then white male hero archetype #1 shows up to "rescue" her, and she is forcefully ejected from heaven and ends up in hell/Odessa.
Hypothetically, the being we'll call Coop (aka Richard) has always been on a mission to save the being we'll call 'Laura', because she's needed to fight the entity invading the Lodges. He travels many worlds. He works for the Fireman, assumes an identity and history when he gets to a particular world.
In the Twin Peaks pilot, by the time he reaches the Laura entity, it's too late and she's already dead. He doesn't recall his Lodge identity fully, forgetting important details from his dreams. He later gets stuck in the Red Room while a rogue version of him runs riot in the Twin Peaks world.
Another entity - his partner, generally known as 'Diane' in the Twin Peaks reality - has also been replaced by an evil double and has to be located. For that matter, briefly diverging, was Maddie Ferguson a tulpa of Laura, similar to fat Dougie? Everyone forgets her when Leland dies. She's never really mentioned again in Twin Peaks and she isn't referred to at Leland's funeral, which is odd. We only see an evil version of her in the final episode of season two.
Laura 'ascended' at the end of FWWM, but she returned to speak to Coop at the start of season three, 25 years after season two. She's ripped away in front of Coop, possibly destroyed, because something evil invades the Lodge. So I don't think 'white man bad' applies, because that wasn't Coop ripping her away.
The point of season three is that Cooper has to assemble a team to battle the invader. He has to rescue Laura, meaning he has to get back into the Twin Peaks world, in spite of his evil double replacing him. Ultimately, Coop time travels to the night Laura died to rescue her at that point, because she's doomed after that by the thing that invaded the Lodges. In doing so, Coop takes the... ahem... nuclear option and erases the events of the original two seasons of Twin Peaks and the end of FWWM. Laura is still ripped away from him in the woods, thrown into another reality, but that's not Cooper's fault either. When Coop/Richard and Diane/Linda get to the Odessa reality, Carrie is still alive (having killed a man who looks a bit like BOB, possibly becaise that universe's version is more vulnerable), which I think is important to whatever happens next. Like I say, I think the beings now known as 'Richard', 'Linda' and 'Carrie' have a job to do either in the Odessa reality or in yet another one. They also need to recruit that reality's Gordon. So the Coop entity
has rescued Laura entity and they're working together at last. The series finishes with both of them remembering who they are: agents of the Lodges.
I still want to know what Coop was up to for 25 years. He's much older in season three (the Arm has also 'evolved') and Coop has a different hairstyle. I doubt there's a barber's in the Lodges!
So has Cooper been operating elsewhere in the meantime? His meeting with the Fireman implies that this isn't the first meeting of this kind they've had. When the Fireman says 'Richard and Linda. Two birds with one stone' at the beginning of the season, Cooper knows exactly what he's talking about.
I begin to wonder if the Red Room is the 'real world' and everything else in places such as Twin Peaks alters according to what happens in the Lodges. Given there are evidently lots of parallel worlds existing, are Coop, Diane and Laura unique beings that move between them and 'Gordon' a 'constant' being that lives in all of them who psychically connects to all the different versions of himself?
I guess Richard and Carrie's next step will be to find Gordon (or whatever he's now called) in the Odessa-verse, who will remember the original Twin Peaks events, and presumably go and find Linda/Diane. If the nuke shattered reality, I guess these characters have to 'firefight' the demon it released in multiple realities. So a 'next season' won't be Twin Peaks. But at lwast the complete team will be together to battle the monster that is invading the Lodges. Different names, different world, different mission, same target.