Claiming their completion percentages throughout the season were "about equal" isn't very accurate, although not terribly inaccurate. 64.1 > 61.7 in favor of Brady this year.
Now, if you were to compare their career completion %'s you'd have: 63.4 > 58.3 (those include playoffs btw). Again, not about equal.
The important comparison comes when looking at their career completion percentage versus their completion percentage in games against one another. You could say small sample size, but 4 games in 3 years, all Patriot victories by substantial margins, seem to tell a story. Surprise surprise, they do...
Luck Career Completion %: 58.3 Luck Completion % Against the Patriots: 50.3
Brady Career Completion %: 63.4 Brady Completion % Against Luck Era Colts: 63.2
Whether or not they both normally complete a high number of passes means dick all when one guy consistently has seen his performance suffer against the other. So no, "the best we can do" is not look at that one game and assume it was because of ball inflation level.