My simulation disregards it, but
I don't. In this sort of random model, the probability of any (specific) large number not being the sum of two "primes" is extremely small (and decreasing rapidly as the number increases), which means that the total probability of any (at all) large number not being the sum of two "primes" is also extremely small.
In other words: in this model, with probability very close to 1 all large enough even numbers are sums of two "primes".
Let's put a little flesh on those bones. I'll stick with the unmodified Cramer model for simplicity; the tweaked versions are fiddlier but not fundamentally different. The probability that n=a+b is a "good" decomposition is 1/log(a)log(b); this is smallest, for fixed n, when a=b; so the probability that any given decomposition "works" is at least 1/log(n/2)^2. There are n/2-2 of these, and they're all independent, so the probability that none of them works is at most (1-1/log(n/2)^2)^(n/2-2), which is approximately exp(-n/(2 log(n/2)^2)). So the expected number of n beyond, say, 1000 for which that happens is the sum of this for n from 1000 up. Unfortunately neither the sum nor the obvious approximation as an integral has a closed form, but we can compute it numerically; it's about 0.000279. That's the expected number of failures above n=1000, and of course that's an upper bound on the probability of at least one such failure.
So, the probability (in this model) of any Goldbach failures above n=1000 is at most about 0.0003, and therefore the probability of any Goldbach failures at all is at most that much bigger than the probability of any Goldbach failures up to n=1000.
Note that although this is a statement with probabilities in, the probabilities aren't fractions of the integers for which Goldbach fails.
The situation is analogous to the following. Suppose you flip a coin 10 times, then 20 times, then 40 times, then 80 times, etc., and for each group of flips you "win" if you get at least one head. Then, with probability about 99.9%, you always win: the probability of failure in successive groups drops so fast that the contribution to the overall failure probability from all groups other than the first is tiny.
Similarly, with the Cramer-model analogue of Goldbach's conjecture, the probability that the conjecture fails "at n" decreases so rapidly with n that almost all the probability of there being any failure at all comes from the possibility of failures for small n.
And that's why you can get good estimates of the failure probability from computer simulations that look only at finitely many n.