Prior to the Enterprise destroying the Borg sphere in the past, the Borg fired on the surface of Earth, killing and injuring people. Many of the people killed were people who worked on the warp ship.
These people would (obviously) do no more work on the warp project, and have no future children. I assume that Lily was one of the three people aboard the warp ship when it made it's first flight, that both Riker and LaForge were on the flight means (imo) that the person who originally was the third crewmember was killed (or injured), otherwise they would have been in the position that they were trained for. With only Lily having to be replaced.
Removing that many people from the on-going timeline, several of them talented warp designers and engineers, had to have had some effect on the future.
I'm sticking with the position that this is a predestination paradox. The Enterprise
-E (and the Borg) were always part of those past events. There was never a timeline where they were not. So no matter how many people on 2063 Earth were killed by the Borg, they were always killed. There wasn't an "original" timeline where they survived. And thus the Phoenix
was always crewed by Cochrane, Riker and LaForge. You can't prove this wasn't the case, after all...
And since they returned to the same future they left, it would seem to support this opinion.