You say "very likely" etc, I say "find the average case and remove randomness from your model".
Essentially the prorate on Bio II means, there will ALWAYS be one tick, and a SLIGHT chance of 2 ticks.
Similarly, for miasma, there is a decent chance of 1 tick, but not guaranteed, which you already agree with.
When taking the average case, we can assign expected values to the damage, and the expected value is not "very likely" it is "average case", which means out of 100 bosses you'll maybe get 90% with 2 ticks and 10% with 1 tick, but the model already takes that into consideration.
I'm not sure what the deal is here.
Lets give another example, a simple one, with just 1 dot.
I cast my dot, then wait 4.5 seconds.
So basically you have
[0-2.5] - no dot
[2.5 - 7] - dot
Now how much damage did that dot do?
It has a chance of two ticks (if first tick is between 2.5 and 4 sec, or to be more precise if the first tick is between -0.5 and 1 sec, so that the second tick with dots is between 2.5 and 4 sec), and chance of 1 tick (if first tick is between 4 sec and 5.5 sec, or, to be more precise, if the first tick is between 1 and 2.5 second, so that the second tick with the dots comes up between 4 and 5.5 sec).
So instead of going, at 7 seconds, it has a 50% chance of 1 tick and 50% chance of 2, you say, okay, the time the dot is active is 7-2.5 = 4.5 seconds.
This is equivalent to an average case of 4.5/3 = 1.5 ticks, and we multiply damage. Will you ever get 1.5 ticks? NO. But you will get 1 tick 50% of the time and 2 ticks 50% of the time.
This is an appropriate method of finding expected value of dots when their application times do not sync up...otherwise you use terms like "very likely", and you have fuzzy math.
EDIT: I also want to clarify why I chose 6 seconds as the "stopping point". At 6 seconds you are guaranteed EXACTLY 2 ticks, no more, no less. So, we can guarantee 2 ticks for the tridisaster model. By also prorating to 6 seconds, we guarantee that our model of "ticks every 3 seconds" now syncs up, regardless of how we applied our dots, so we no longer have to prorate anything. We assume at that point onwards all dots are ticking for both models.