This is mainly the reason for the different rotations. Both of us are basing our rotations off of Simulationcraft simming (though im giving general info and they include the T13 bonus) and i just listed other things i thought important. Doomguard for instance is VERY important and i dont want anyone forgetting it.
The source we both use for 99% of what our guides say:
Go to affliction and check action priority list.
There is a bit of flexibility in our specs. This is why i go over mandatory talents and optional talents.
My spec includes CoE which is nice for leveling, heroic 5mans, pvp and if you are like me and end up in groups where no one is brave enough to kite an add (Think of the adds in the last boss of BRC) or has a slow when one is needed (riplimb from Shannox).
In theirs they include 2/2 drain life which makes it where you healers wont have to heal thru Lifetap as much and makes you less likely to die from incidental aoe.
Which is better depends on the needs of your raid and your playstyle. Back when i posted the spec we might have been expected to kite some and i felt for your new 85 lock CoEx was a better choice. But this tier there is few places id use it (maybe on Sappers on Blackhorn).
The BIG Difference in our specs comes down to SB:SoC vs Pandemic. Pandemic is a WEAK WEAK WEAK single target dps increase. SB:SoC is a POWERFUL AoE ability for a spec that is not that great at aoe. I feel that SB:SoC is better (think of all the adds Yor for example) but if you want MAX single target Pandemic is the talent to get.
Ultimately the difference between our specs is utility. They are going for maximum single target dps and survival, while my spec trades SMALL amounts of damage for more AoE and a fun utility spell.
None of this will affect your rotation though.
Bane of doom should only be used in situations where you know the mob will live longer than 15seconds and which you dont plan to use soul swap on.
Bane of doom takes 15 seconds to tick and for all intents and purposes can not gain extra ticks. Bane of agony ticks every 2 seconds or less and is the easiest spell to get extra ticks through haste. Bane of doom is more single target dps (can only be on one target).
Because of this if the targets lives less than 15 seconds you wont get any damage from BoD meaning its a 0 dps spell (actually its negative as you waste a GCD on it). Agony though can tick 7 times or more in that time making it a MUCH better spell to use in that situation.
Also, since Doom can only be used on one target at a time soulswapping a target with doom is a dps loss (soulswap saves you at most 1-2gcds) and you LOSE that gcd having to manually apply agony to the target you SS off of.
This is why Agony, despite the ramp up time, should mainly be used on trash and doom on bosses.