Out of state tuition can be pretty complicated. Let's first look at the converse situation and compare an athlete who is subject to out of state tuition to one who is a state resident.
If the total of tuition, fees, room/board, and $400 for books is $40K for the out of state player, and $20K for the in state player, and the out of state player gets $10K of athletic aid while the in state player gets $5K, then both players are getting 25%. The D1 Manual doesn't distinguish between in state and out of state players, but the procedures for the exact calculation of equivalencies does require a separate computation for in state and out of state players. (BTW, the 25% minimum and equivalencies in general are not based on the COA, which is typically higher than the costs listed above.)
Now, how about a waiver? Here are some possibilities--the waiver is:
1) given to all students who are resident in states that reciprocate waivers
2) given to all students that meet some non-athletic qualifying standard like GPA
3) given to all athletes
4) given to one stud baseball player.
For 1) and 2) the amount of the waived tuition clearly won't count toward the 25% or 11.7
I suppose that 4) would constitute athletic aid, and would count.
I suspect that 3) would depend on the exact circumstances of the waiver. My guess is that if the waiver is granted unconditionally, and can't be withdrawn, it wouldn't count.