His concept art also showed the Derelict. He'd also spoken about how much Alien: Isolation had effected his work on the project. He's also said he's a huge fan of Alien, of the psycho-sexual aspects of the series.
And besides, Alien Resurrection had a Queen, AvP had a Queen - that didn't equate to Aliens 2.0. The return of Alien equipment is visual continuity too - something people have an issue with Prometheus for.
Prometheus did not copy Alien's designs, except for the Derelict and Space Jockey, kind of essential if you are making a prequel revolving around them. There was no Nostromo Mark II in Prometheus. There was a flamethrower, though, not exactly a weapon unique to Alien but fair enough.
Wasn't that a huge complaint about Prometheus is the lack of visual continuity?
Yes, A:R had a Queen, that's about it. No pulse rifles, no dropships, no colonial marines. A:R is its own universe.
AVP and AVPR are fanboy movies. Anderson is a big fan of Aliens, hence all the references to Aliens and the inclusion of the Queen for the big finale. AVPR has a mock APC and Ripley/Newt. But obviously, being set in the present day, they couldn't have dropships and pulse rifles. Neill's film would have taken this fanboyism to the next level.