BOAC, with respect, if it's in the JAR or EASA regs, then the Chief Pilot has no discretion - it's the law.
For the OP, my understanding (in Europe) is that for the carriage of passengers the pilot(s) must have done the requisite 3 landings and take-offs within the 90 day period. Note, not just commercial - it applies to PPLs as well.
As a freelance you still have to comply. Yes, pay if you have to; a generous employer might let a freelance do it without charge, but honestly that's probably dreaming.