Company X maintains a cafeteria plan for its employees. LTD coverage above a base line percentage of pay is paid for by the employee with pre-tax salary reduction contributions. LTD benefits are self-funded using a nonexempt welfare benefit fund. Do the employees' pretax contributions to the LTD coverage have to get taken into account for purposes of determining the 419/419A limits?

Yes, although the calculation is under 419, not 419A. Section 419 provides that "[th]e term “qualified direct cost” means * * * the aggregate amount (including administrative expenses) which would have been allowable as a deduction to the employer with respect to the benefits provided during the taxable year, if— (i) such benefits were provided directly by the employer * * *."