A conceptional and numerical comparison of one parameter generator coordinate method (GCM) and quantised adiabatic time-dependent Hartree-Fock (ATDHF) theory is performed by applying both theories to the "C + "Ne and l 6 0 + l 6 0 system. Different parametrisations of the Skyrme interaction are used. The single-particle wavefunctions and the operators are represented on a three-dimensional grid in coordinate and momentum space. The collective path is evaluated in the gradient method, corresponding to GCM, and by solving the numerically more involved ATDHF equations. The potential, translational and rotational moments of inertia are calculated along these collective paths as well as the mass parameters corresponding to relative motion. As the next step, the quantised collective Hamiltonian is extracted from the collective path and subbarrier fusion cross sections, as well as astrophysical S factors, are calculated by means of generalised WKB techniques. This allows discussion of the differences between the various methods at a significant and sensitive physical quantity. Whereas for the doubly closed system l6O + l 6 0 the GCM turns out to be a rather good approximation to quantised ATDHF, there are significant differences in the doubly open '*C + *'Ne system.