When Larry Coon said that free agents cap holds are excluded in "Sign-and-Trade transactions", they are excluded just to determine if a team can receive a player in a S&T. With the new CBA, a team that is a above the apron ($4M above the luxury tax level) can't receive a player in a S&T.
Free agents cap holds are not removed to match salaries during the S&T. S&T rules are exactly like trade rules. It's 150%+100K (not all the time but doesn't matter) or the team must be within $100k of the salary cap after the trade.
In Spurs case with Bonner amnestied, and empty AK47 S&T would let Spurs in the follwing situation:
Tony Parker: $12,500,000
Tim Duncan: $10,361,446
Boris Diaw: $4,702,500
Danny Green: $3,762,500
Nando De Colo: $1,463,000
Kawhi Leonard: $1,887,840
Patrick Mills: $1,133,950
Cory Joseph: $1,120,920
Aron Baynes: $788,872
Manu Ginobili: $6,746,988
Splitter's cap hold: $7,493,600
Kirilenko salary: $X
Total: $51,961,616 +$X
If you take a salary cap at $58.5M, Spurs should be at max at $58.6M which makes Kirlenkjo max possible salary at $6,638,384.