Typical of HMRC - staffed as they are by those who are not a success in the accountancy / tax profession, they victimise and target any individuals perceived to be successful or seen to be using legal loopholes to their advantage.
I wouldn't assume they know what they are doing, nor that they know they are discriminating between marine and aviation. Someone in HMRC has seen a stream of revenue from pilots that is untaxed, and used the "unfair" argument to further their career.
I doubt that if anyone had the money and time to challenge them, that it would stand up in court at all.