You are correct. The Tribunal does not have the authority to override Acts of Parliament, such as the Pension Act. But it doesn't have to, in these cases.
A great deal of the testimony in the recently completed remedy hearing dealt with what the actuaries call "unwinding" of the pension plan. Unwinding is simply repayment of pension proceeds, then deduction of pension payments that would normally have been made in the course of the employment that was denied. The net effect is to put the person back into the position that he or she would have been, absent the wrongful termination of employment.
Once the pilot is back on the payroll, then the pension deductions would resume normally, to the date at which the individual acquires 35 years of service, where contributions cease. The pilot does not receive both a pension and a wage--only a wage. When he or she eventually retires, the pension would then be paid on the basis of the factors accrued as of the date of retirement.