I was mobile when I wrote the original question - perhaps a better way of phrasing it would have been something like:
Don't many (most? all?) of these theoretical approaches assume that the sequence of results for each page (call them a_i and b_i for i=1,2,3... where each x_n is 0 [no conversion] or 1 [conversion]) are sequences of iid random variables with underlying conversion probabilities p_a and p_b? In reality, these sequences are much more complex and, if the scale of the variation in conversion probability within the sequence is greater than the difference between p_a and p_b won't the test be much weaker than we originally thought?
To use an example that is simplified vs. reality but hopefully indicates what I mean, imagine that we have two traffic sources - one with a conversion probability twice that of the other (on each page variant - so p_1_a = 2p_2_a and p_1_b = 2p_2_b). We randomly send traffic from both sources (1 and 2) to each variant (a and b). Do the standard tests work even though our sequence of conversions are not iid?