ssh-keygen DH Primality Testing
In ssh-keygen.c of the OpenSSH source code, there is the following call:

        if (prime_test(in, out, rounds == 0 ? 100 : rounds,
            generator_wanted, checkpoint,
            start_lineno, lines_to_process) != 0)


...and a comment for the function prime_test says:

 * perform a Miller-Rabin primality test


Therefore, it does indeed use a Miller-Rabin test. One can show that for composite $n$, at least half of the possible random choices prove the compositeness of $n$ (in fact, there are even stronger bounds), hence the confidence in $n$'s primality after $k$ runs of that test is larger than $1-2^{-k}$. In the particular case $k=100$, the probability is (larger than) roughly $1-2^{-100}=0.999999999999999999999999999999$, which is a lot.