SEP IRA Contribution limit for S-Corp

A 100% S-Corp owner wants to make an employer SEP contribution, which can be no more than 25% of W-2 wages from the S-Corp. Box 1 of his W-2 includes $7000 of health insurance premiums and $3650 of HSA contributions paid for by the S-corp, neither are subject to fica or medicare tax. Is the 25% employer SEP limitation based on Box 1 wages, or is it limited to wages subject to fica and medicare tax indicated in boxes 3 and 5? IRS publication 560 ,chapter 1 suggests that these fringe benefits can be included for calculating the contribution limit and my CPA is of the same opinion, however an IRA specialist I spoke to contradicted that notion saying that if the fringe benefits resulted in an adjustment elsewhere ( in my case they are deducted on the corporate return) then those fringe benefits cannot be included for purposes of calculating the contribution limit and boxes 3 and 5 of the W-2 ( income subject to social security and medicare wages ) should be used instead. Could you please clarify this as I have been using box 1 for two years and don’t know if I should be correcting excess contributions as well as what to do going forward?