According to the rules currently posted there is a difference between the girls and boys but only for the U-15 age group. U-15 boys are allowed 7 subs with re-entry allowed, U-15 girls have free substitution. Rules for U-16 through U-19 girls and boys both restrict subs to 7 per game, no re-entry allowed.
At the U-15 level the 7 subs with re-entry allowed rule for the boys has minimal impact, because the roster limit for the U-15's (girls and boys) is 18 players. However, the U-16's through U-19's have roster limits of 22 players. Any team in those age groups carrying more than 18 players will not only have to deal with the "no re-entry" rule, they will have to deal with 1-4 players per game never setting foot on the field.
As a major showcase tournament you will find many DII and DIII colleges there that will not be realistically looking to recruit the "best of the best", which is why everyone should get some opportunity for playing time and exposure in a tournament of this type.
I'm not sure how many of the clubs are aware of the rule. The application deadline was Aug. 15, the posted rules are dated Aug. 25, and the Labor Day qualifying tournament was played using free substitution for both genders, all age groups.
Good points have been made in this thread arguing the merit of limited substitutions as incentive to player effort, as well as preparation for next levels of play. However, as a showcase tournament I think this new rule will have many teams reconsidering the value of attending the tournament in the future. Unlike the college, professional, and national team levels, Disney is still a youth soccer showcase tournament where mom and dad are paying premium freight for participation and more importantly exposure.
I hope that by the time the tournament arrives, the team managers will be told by tournament officials at the team check-in, "by the way, the rules have changed, we're allowing free substitution"... same as you'll find at the Raleigh Showcase (also co-sponsored by Chelsea).