The language in the employment contract describes the how the company will determine how to calculate the compensation to be paid to the HCE.
On the surface, it appears that the company is including an amount in the HCE's compensation that is equal to x% of compensation which is added to the HCE's gross pay and labeled "pension funds". Since it is added into gross pay, presumably payroll taxes are being withheld from the "pension funds".
The HCE has filed an election to defer x% into the plan.
Check to see if the plan definition of compensation includes this special pay. Some plans have definitions that specify certain categories of compensation are excluded from the calculation of deferrals. For example, if the "pension funds" are given to the HCE in a lump sum amount at the end of the year, the "pension funds" will look more like a type of bonus and the plan may exclude bonuses. As an aside, ask if the "pension funds" are included in compensation for purposes of the company's other benefits (for example, life insurance coverage as a multiple of compensation).
Also check whether the x% is applied to compensation before the "pension funds" are added to compensation, or is the x% applied to compensation after the "pension funds" are added to compensation. Self-referential formulas are a pain. If the deferral is calculated before the "pension funds" are added and the "pension funds" are included in the plan definition of compensation, there may be an operational error for failure to follow the HCE's deferral election to defer x% of compensation.
If the plan is a safe harbor plan, then hopefully the "pension funds" are included in the plan definition of compensation. The definition of compensation for calculating a safe harbor contribution likely will require the inclusion of the "pension funds" in the compensation used to calculate the safe harbor contributions (match or NEC).
Since the HCE was able to negotiate this special deal, I suspect that there is a good likelihood the HCE will hit the deferral maximum. Does the contract address what happens if the HCE cannot defer x% of compensation due to the annual maximum deferral limits? Is the annual compensation limit taken into account when calculating the x% of compensation? The company and HCE should have an agreement on what happens should limits prohibit deferring the full x%.
You are correct to be concerned because of the potential operational errors that could result from ambiguities in calculating this HCE's compensation and deferrals. With some good luck, none of this is an issue.