I think what Blomkamp means by having it be connected to ALIEN and ALIENS, is that the events in the film will directly relate to those events and not necessarily cast out the events in the other films. For instance, the derelict perhaps...
There is a simple way to explain the timeline issue.
The easiest way for it to make some sense is if the scientists lied to Ripley 8 and Weyland-Yutani IS the government or needed the government to fund the experiments. They were 'operating outside of regulated space' after all, so... Since W-Y headquarters features prominently in Blomkamp's concept art and in A:R Ripley is told the company doesn't exist anymore that would have had to of been a lie.
Building on that, it's entirely possible to say that the Scientists who wanted to keep the Ripley 8 clone alive, were working under orders from the company that were hidden from the military operation, like ASH in Alien had orders the rest didn't know about. Here's the trick: They were also lying about a lot of things to Ripley 8. For instance, about it being 400 years later, so she would feel hobbled and alone, during their studies and wouldn't try to contact anyone and be more likely to give up info. Sort of like the lies we tell terrorists and suspected criminals during interrogations.
That would also explain Hicks. As a matter of fact the film could open with Ripley 8 locked in a lab, tortured and being tested on by the company, trying to figure out how to use her DNA or reverse the effects of the black goo on someone and have Hicks come and rescue her. It would be very easy to explain that lie to her, or by that point she could just know.
That said, I believe what Blomkamp means to say is that his film will relate directly to the events in the first two. And that if anything, A:R separated itself from them and he will return to that. The above would also explain how ripley is no longer 'categorically' ripley 8.