If you do not opt out you will not be recognised as self employed and it will cost you more money as you will have to pay employers social insurance, you would not be able to claim expenses against tax and, most importantly, you would be in breach of your contract which states (in two different clauses) that you should not be considered an employee of the Contractor (McGinley Aviation).
If a pilot opts in then he is deemed to be a McGinley employee. If he is an employee then he cannot be a director of a limited company.
Not sure what your contract says but older contracts had written that you will not at any time be deemed to be employees of McGinley or Ryanair.
So basicaly if you opt in, you were in breach of the contract. Although they give you an option, there is only one right answer. Hope it helps