In ceres::CostFunction::evaluate(double const *const *parameters, double *residuals, double **jacobians) (see link), the Jacobians are provided thru a "row major" array.
This is important only in the case of analytical factors (factor_analitic.h L105) in which this array is mapped using an Eigen::Map<Eigen::Matrix>.
The API of the factors is going to be redesigned. Most probably, using Eigen::Map<Eigen::Matrix> over some ceres::jets that also contain the Jacobian rows. Then I think this storage order is important to be maintained.
Indeed, now manif and wolf are incompatible because of this.
We can possibly assume that transferring matrices from row to column major could be doable at small scales (like the jacobians of any of the factors). The questions is what to retain as default.
Personally, I would like to have the same default as Eigen, but I still do not see the implications (either positive or negative) of changing it.