I suspect they had a increase in four day badges vs one day badges. As has been pointed out unique attendees is not as useful as turnstile. 50k single day spread out over four days with 10k four day has a lot less impact then 50k four day with 10k single day. Hence the need to cap badges.
Their media page says: "ninth consecutive year of record turnstile attendance, reaching 207,979, an approximate 4% increase over 2016", which is where the 4% comes from (turnstile). I don't remember them releasing a turnstile number in any previous year.
"“We made a decision early in planning Gen Con 50 to optimize the attendee experience while still continuing to grow the convention to new attendance levels,” “By adding the field level of Lucas Oil Stadium, improving space planning, and carefully restructuring attendance thresholds by badge type, we realized record gains, while maintaining a world-class experience for attendees.” [my emphasis]
If you are right that they increased four day badges, how do we explain that the sell-out of 4-day badges happened so early? There was not significant growth from 2015 to 2016 to imply that this would happen (uniques actually went down). Because the sell out happened early, I was hearing some speculation that they were trying to cap 4-day to make more money on 1-day badges, which is the opposite of your theory.