Previously I use EIGEN_MAKE_ALIGNED_OPERATOR_NEW for self-defined class containing fixed-size Eigen objects, but now I find this is too error-prone. Now I want to use EIGEN_DONT_VECTOR to get rid of this problem, do I have to remove the existing EIGEN_MAKE_ALIGNED_OPERATOR_NEW?

Also, I used Eigen::aligned_allocator<gtrk::Hyperimage> at several places, do I also have to remove them, after I defined EIGEN_DONT_VECTOR?

You do not have to remove them, they only become useless.