You WANT it at 90 degrees during operation, but wither that equates to having the individual pieces scraped to 90 degrees depends on the mill in question.
AFAIK, sag from weight/gravity would be the primary reason to scrape at another angle, so if it was me, I would inspect the individual pieces on granite and see how square they measure, and then assemble it and see if there is a difference.
In some cases, you may also need to consider the load when cutting, but in general I would consider that as designed into the mass and shape of the castings. IOW, if it's lined up perfectly before a cut, and is flexing whatever amount while cutting, it's not an alignment issue so much as a using-too-hard issue.