Testing a rotation at 2.43s isn't relevant when none of our BiS builds have that much spell speed to begin with. 2.5s and 2.48s are the primary BiS builds (and theoretical highest damage potential), if it's not even consistent on either of those 2 GCD tiers then there's no argument to begin with before we get to potency comparisons.
"if you hold Aetherpact until the middle of the GCD cooldown, it won't be applied until at least 1.5secs later"
This isn't how it works exactly. It really just boils down to where your pets "GCD" is, and how soon it can weave Devotion once it's commanded to. Devotion timings are never 100% consistent because of this, with REALLY good execution you can generally keep it contained within the window of 1 GCD worth of time, but you can't guarantee it will ALWAYS occur at the exact same place. This is also where your GCD build comes into play, because your GCD alignment will differ slightly compared to me testing this at 2.48 (and for me, that Devotion is casting nearly instantly with how you're proposing it).
"the difference in DoT damage depends on how many DoTs tick via a Bio and Miasma refresh before a boss jumps"
The only thing that matters when it comes to a situation like this, is whether you can avoid a hardcasted set of DoTs or not. The number of DoT ticks will always be the same, it's just where those ticks occur. You can then take it a step further and include the potential of gained Tri-Disaster casts, as they provide 300 potency up front now (by gained, I mean using a Tri-Disaster before down time, provided the down time is long enough that you'll gain the next cooldown in time for a boss to return). However you never clarified on either of these points.
"you then get a difference of 47.9 potency, again, in favor of the delayed opener"
From where exactly? It's already flawed that you shown 2 images of different length (you took my opener and reduced it down to 13 GCDs, yet what you created is 16 GCDs long). So are you attempting to compare a 13 GCD sequence to a 16 GCD sequence? Because according to the rotation sheet we use, all of our openers come out ahead in a 16 GCD sequence compared to yours (with me attempting to correct what you've edited, and even giving you the benefit of the doubt of 2x akh morns hitting Devotion with an actual BiS build).