One problem...
I never said any of the things you just claimed...YOU are the one that said that.
I said THIS...
"... a boss mob can have a random choice of which of its attacks to use. It could be a tank buster, it could be a gaze attack it could be something else. Either way all of those will disrupt your timing, which in turn causes you to alter your rotation to something else."
None of that was about phase mechanics.
I stated...... that the flow of combat was going to dictate your rotation dependent upon how many of these mechanics (and boss attacks) target you and whether or not the phase transition was based on Boss Mob health and Party DPS output, just as you mentioned in the second part of what you talked about.
That was the very reason you used to have to blow your Deathflare early back then, because you'd hit near that transition point and all the BLMs would kick in their Enochian, your previous 20 second window became a 6 second window before the transition happened.
But it varied because if there weren't any BLMs or the DPS's were just plain crappy, your 20 second window was very safe.
EDIT:
Fair enough... I'll give you a specific two specific ones.
1. That Gaze Attack, if it hits during the time you're running your Trance and you've only got a good 6 seconds left you my have to blow your Deathflare early... so all of those rotations you meant to do while you were in trance are gone and have to be skipped.
2. A specific mechanic is in the Dun Scaith, you could get tethered to a Hand... which will chase you at super speed unless you turn around and face it to stop it. It will kill you instantly if it reaches you... and it will only stop for a certain period of time even if you face it.
You better kill it quick. So you're probably going to have to blow your Festers on it... they are gone at that point. If these were supposed to be in your rotation at a later time, they're now gone and you're going to have to alter your previously planned "rotation".