BUG: Correct issue if patsy handles missing. Closes #2083.

needs a unit test.

Are endog and exog here still the full length? I thought they will be the ones shortened by patsy. In that case, nan rows because of nans in extra arrays would require to drop additional rows from endog and exog.

(It's a pain that we cannot turn off patsy's missing handling. I don't think it will currently be very common to have extra nans in the extra arrays, but we have two multi-equation PR's betareg and heckman, and more will be coming for which we will have to check nans across several separate design matrices.)