Boundary roughness scattering in disordered tunnel-coupled quantum wires in the presence of a magnetic field is considered. The low-temperature conductance as a function of applied magnetic field is calculated for different structure and disorder parameters using the method of the generalized S-matrix composition. We show that despite the fact that lateral wire width fluctuations of the size of few atomic layers may significantly shift the partial energy gap, the effect of the conductance enhancement at energies in the partial energy gap does take place in sufficiently strong magnetic fields and small correlation length of the disorder defined as the average distance between the neighboring discontinuities of the boundary profile. The last parameter is shown to be particularly important for the determination of the transport properties of the system. Remarkably, we find that in a wide range of system parameters the conductance decreases with the correlation. length despite the decreasing number of boundary discontinuities.