The employee's deferral is considered to be from the employer. All funds put into an HSA by an employer are considered as being from the employee for purposes of the contribution limit. There are not separate limits. If the contribution is only from the employer, it still counts towards the employee's contribution limit. And if the employer makes a late deposit, by April of the next year for the prior tax year, it shows on the newer W4, but still counts to the prior year's limit.