Lets say we have a situation like this:
Wait 40,000: spawn unit A, preserve
Wait 60,000: Spawn unit B, preserve
Wait 70,000: spawn unit c, preserve
With hyper triggers.
It will wait 40k, spawn unit A. Then, it goes to the wait 60k, and as it starts to wait it checks all other triggers above it to fire, so it has to wait 40k again. Then it finishes waiting the 60k and spawns unit B. Then, for the 70k, it waits the 40k, waits the 40k again because the 60k wait had it check the order again, finishes the rest of the 60k wait, and THEN waits the 70k, THEN spawns unit C.
I THINK that is right. Even if it's not completely accurate, that's the general basis of how wait stacks work.
You said all triggers with waits (are supposed to) fire at same time. Make this one trigger and you're problem is solved