The exact interval used by -ci, binomial- is the Clopper-Pearson interval,
but you must realize that "exact" is a bit of a misnomer. It is exact in the
sense that it uses the binomial distribution as the basis of the calculation.
However, the binomial distribution is a discrete distribution and as such its
cumulative probabilities will have discrete jumps, and thus you'll be hard
pressed to get (say) exactly 95% coverage.
I do not think this is correct. For the CI, it is the parameter space, not
the sample space, that matters (and the former is continuous). In other
words, if we have k successes out of N trials, we are looking for limits
{p_l, p_u}, such that