CJRS - HMRC Calculators for claims of NI & Pension element

Has anybody else noticed the disparity in the HMRC calculators for furlough claims when the employer tops up the pay. For NI purposes the ni free allowance is deducted from the total gross pay ( furlough + top up) whilst with pensions the lower limit is deductedin full from the furloughed amount only. Is there a logic that I am missing?