I think there is a certain amount of truth in extra legroom seats attracting the higher rate of APD, depending on the exact interpretation of the legislation underlying the APD tax. I recall when BD scrapped "business class" and introduced "economy extra" (which was equivalent to business class in all but name) there was talk that "economy extra" should attract the higher rate of APD. I don't think it ever happened that the higher rate of APD was charged. The legislation does not speak of "cabins" per se but does refer to enhanced or upgraded levels of service, even within one cabin.
It may be that APD has nothing to do with the LS decision to remove extra legroom seats as Aer Lingus and easyJet certainly dont charge extra APD on their extra legroom seats.