It is of course not entirely true most places that 'no one skips the security line.' if that refers to the very long lines you see at the Louvre or d'Orsay etc. There are separate security lines almost everywhere for people who hold the pass. This is true at the Musee d'Orsay (where often there is no line at all for pass holders who just walk in their designated door, in high season the line might be 15 minutes compared to the non-ticket holder line of a couple of hours). At the Louvre pass holders can use a separate line at the Pyramid; it may be quicker to just go through security at the Carrousel entrance. There is a passholder/ticket holder line at the Orangerie, the Pompidou. There is no security line advantage at Versailles, the Notre Dame Tower or Sainte Chapelle. The kids will probably want to climb the Notre Dame Tower so you get reserved time slots early the morning you wish to visit either by Ap or at a machine at the site. You then return for your time reservation.
for the Eiffel Tower, reservation holders use a different elevator and you will go up very close to your time. The trip from level 2 to the top requires new lines for that elevator and that does not have priority; everyone queues in the same line.