Maybe it's just me, but that guy seems to overestimate the importance of the game.
I figure it's just that he's fairly new to the Trek tie-in business. Various novel and comics companies have been doing tie-ins for decades, and the canon has never been bound by anything that happened in them, nor indeed have other tie-ins been bound by them. So really, why shouldn't they be allowed to make changes? And it's not like CBS ignores any of it. They're just a lot more flexible these days than they were in the past.
Indeed, I get the impression that Brannon Braga's Hive
miniseries for IDW is making some major changes in the status of the Borg and a couple of canonical characters, much as Pocket has done in its books. So maybe he's wrong to assume that STO wouldn't be allowed to make a similarly major change; maybe it's just that they haven't tried yet.