When I wrote the "Q Who" observations article for EAS some weeks ago, I only noticed that the reaction shot of the Borg in main engineering was different and covered that shot in the upcoming article. I didn't notice all the other new shots but I will update the article accordingly and give you credit, Tosk.
I contacted Mike about this and he acknowledged the difference but didn't say anything else.
I assumed it had something to do with the software they used to identify the correct film elements. I cannot think of another reason why so many shots in a single scene are different.
Should anyone find more cases of different takes/shots or any other things that would be of interest for the observations articles at EAS, please let me know and we will include the observation and give you credit for it.