K, uhh...
We kinda had this problem before. And we ended up not deciding on the matter, because other technicalities "solved" the issue. See the third (unasked) question here:
http://www.smogon.com/forums/threads/substitutions-and-cooldown.3539003/.
Regarding this situation, and considering the wording of the new sub rules, I would argue that what counts is actual activation, not just the fulfillment of the requirements. That is due to two things:
1) The Handbook states that: "The result of a Substitute's "activation" can be changed by instance, but the trigger never changes.". I am reading that as "The result of a Substitute's "activation" can be changed by the instance of the "activation", instead of "The result of a Substitute's "activation can be changed by the instance it is triggered". So what matters is that the sub must activate, not only the trigger fulfilled. There is a difference between the both, as I will show below.
2) The second rule says that "Substitutions either activate, or they don't." and the third says that "Substitutions activate whenever the trigger's conditions are met,
and the result of that activation is legally usable". The bolded part means that the result of the sub activation must be legal, which means that both:
a) The "Action Clause" (second half of the sub) must be legal
b) The sub can legally activate in those circumstances.
I will get somewhere, so keep up with me.
The second meaning is what matters here. When a sub activates, the action-set is changed. The second rule says that it either activates or not, so the middle term "activates but doesn't actually activate" isn't possible.
This is actually a result of a council voting. See here:
http://www.smogon.com/forums/threads/substitutions-overhaul.3519902/#post-5883336
To sum up the old shit: there was once a proposal to enable "two or more substitutions activate on a given situation, as long as there isn't any conflict between them". The proposal was DENIED by the council, which basically means it said that "only one substitution can activate on a given situation. If no priority is said, then the first sub will activate in detriment of the second and third". The reasonings brought on the posts make me draw said conclusion. This means that it is illegal for two subs to activate at the same time, so only the top one activates and the bottom one doesn't as per third rule.
So we get that:
1) The Result of a substitute can change based on the instance of its activation, not of its trigger.
2) When the trigger of two substitutions is fulfilled at the same time (read: 2 or 3 subs CAN activate), only the top sub WILL activate. So the bottom sub CAN activate, but WON'T. Because the council once decided that two subs can't activate at the same time.
So yeah, my "ruling" would be that a Clear Smog+Clear Smog ~ cool down ~ Venoshock action set would make Granbull use 15hp sub - EQ - Dig.
BTW, even I admit that this isn't the most reliable ruling ever, so it might be adviseable to poke the council to decide specifically on the matter. Also because it has amusing repercussions. For example, consider the following sub:
Surf - Surf - Surf
IF Thunder Punch THEN Acid Armor on the first instance, Counter on the second and push back
If the opponent answers with Taunt - Thunder Punch - Thunder Punch, we will get two different possible outcomes:
a) If the instance is of the trigger occuring: Our pokemon will use Surf - Surf - Counter, since on the second time the trigger occurs, the result of the sub is legal, therefore it can activate just fine, even if the first instance was illegal.
b) If the instance is of the sub activating: Our pokemon will use Surf - Surf - Surf, since the sub never activated due to the result of the first activation is illegal.
dunno which option should be emphasized tbh. One of the advantages of not being on the council is that I don't need to care about that haha.