The FTO system has AIUI always "lobbied" against N-regs.
But IME it was usually in the form of spreading dirt at every opportunity. Even UK AOPA, with its large number of corporate members, was very ambivalent on this topic for years - until they got in line behind N-reg, very recently.
The question is what exactly are the FTOs doing now? Are they paying a professional lobbying firm in Brussels? Now, post-EASA, that's where it matters.