It is perfectly permissible for an employer to say that your compensation package includes your benefits. Let's say your "total package" is $200,000. So, if your health insurance is $20,000 a year paid by the employer, the employer is going to set your W-2 compensation at a number that is reduced by that expense. Likewise, other items might be included in the gross calculation but not in your "paycheck", like company car, continuing legal education, country club dues, etc etc etc.
We have lots of legal and medical practices where the total compensation package approach is used (I teach my clients to use it!) for their more high paid individuals. And if one of those docs or lawyers is getting a company contribution into their 401(k) of
$35,000 to maximize their 415 limit, that is $35,000 that is NOT paid to them in their W-2. If they are not in the plan, then that $35k is in their paycheck. Your 3% might be being treated in exactly that way, and there's nothing wrong with that so long as you don't have an employment contract that says otherwise (our clients' have employment contracts that explains that their total compensation package provided to them INCLUDES these specific items). It appears they are doing a salary REDUCTION (not a salary deduction) and that's the way it would be handled. If that is what they are doing, it is NOT a violation of any of the safe harbor provisions. You are getting 3% of your (let's say) W-2 compensation allocated to the plan. It's just that your W-2 is lower than it otherwise would be, and yes, you are effectively funding your own 3% contribution.
We did the same thing many years ago (and still do with the 3% safe harbor) with regard to rank in file employees. When the plan is established and we have to give employees 3%, we may tell employees that BECAUSE we are installing a plan where they will get 3% contributed, THIS YEAR we are forgoing our regular 3% raises to pay for the plan contribution, but only this year. Next year we will be back to regular raises. If you are clever enough to see the math here, you will recognize that the one year lack of salary increases actually pays for the 3% annual contribution FOREVER, not just the first year. As I wrote and said when top heavy came in: "Congress says you have to give the employees 3%; it doesn't say YOU have to pay for it!"