There are two sides of the coin, lets look at the other point of view.
Icestar and I have had words on this HM FP's before.
1) No the final boss in T5 should not be skippable, but it isn't game breaking just a oversight by the Devs.
If you refer to my other thread about gamebreaking so yes, skipping bosses that players really want to do
is gamebreaking. It is content that some want to experience and to have someone scream and start a fight with you for simply want to kill a boss that drops something you need is a negative experience hence gamebreaking, but I already have a thread about that.
They have placed the final boss far away without game mecanics related to completing the flashpoint, I am not sure it is a oversight, I think they simply did not expected players to skip bosses and avoid mobs like they do today.