Using the colour dipole picture and the colour glass condensate effective theory, we study the diffractive production of two or three jets via coherent photon-nucleus interactions at high energy. We consider the hard regime where the photon virtuality and/or the transverse momenta of the produced jets are much larger than the saturation momentum Qs of the nuclear target. We show that, despite this hardness, the leading-twist contributions are controlled by relatively large parton configurations, with transverse sizes R ~ 1/Qs, which undergo strong scattering and probe gluon saturation. We demonstrate that these leading-twist contributions admit transverse-momentum dependent (TMD) factorisation, in terms of quark and gluon diffractive TMD distribution functions, for which we obtain explicit expressions from first principles. We go beyond our previous work by evaluating the contributions involving the quark diffractive distributions and by establishing that their DGLAP evolution emerges via controlled calculations within the colour dipole picture. We find the same expression for the quark diffractive TMD in two different processes (semi-inclusive diffraction and the diffractive production of quark-gluon dijets), thus demonstrating its universality.