Kinberg said Logan takes place in the new timeline as does everything since Apocalypse.
The reason Wolverine remembers the battle on Liberty Island is that he's "The Observer" aka the only person with memories of the original timeline (Xavier was referencing the hotel where Laura and Gabriela were staying, not the climax of X1 since he never lived it).
It would have to though.
The only reason Logan and Rogue meet Professor Xavier, Scott, Jean and Storm is because of the events of the first film! That means Magneto is still looking for Rogue, he's with Mystique, they have the Statue of Liberty scheme, etc.
How do we know it still occurred in timeline B? Because at the end of DOFP in the revised future, we see Rogue is at the mansion and she has her white streak (that she got from Magneto at the Statue of Liberty). Not only that, but Logan is there and Scott, Jean, Beast and Storm recognize him. So the only explanation is, well,
I still love his introduction in the Canadian hillbilly cage-match and his dialogue with Rogue when he discovers her and decides to help her out. It's not mind-blowing but it set a nice tone that sort of falls apart in the weirdly staged rescue that follows.
Is this. It all happened.
The only way Logan and Rogue get to Professor X is via Sabertooth trying to kidnap her for Magneto. That's X1's plot and it's crucial. So even Timeline B doesn't even make sense. Apocalypse Magneto and Mystique team up again after it's clear Mystique wants nothing to do with him in the revised timeline? Magneto is still going to carry out his 2000s scheme even though he and Xavier left off on good terms? None of it adds up. Even something like The Wolverine can't happen thanks to DOFP because one of the catalysts for that story to even occur was the death of Jean Grey, who isn't dead in this new time line! So why is there a sword in Logan?
All these movies are their own thing. None of the continuities make a lick of sense pre-DOFP or post-DOFP and it's clear Singer, Kingberg, Mangold don't really care about any specific timeline and just set out to do their own take and make an individual story that stands on it's own.