Practically these conditions are met if the axes are within half a millimeter of each other. Usually they are. The alignment of the goniometer axes is not adjustable and for practical purposes can be considered perfect. The alignment of the beam with respect to the goniometer is adjustable and imperfect, but does not affect results provided samples and slits are correctly sized. That leads to the use of slits.
Slits are noise control devices.
Detector slits keep stray photons out of the detector. Its direction does NOT depend on sample angle. Only its intensity varies with sample angle. Ideally we would get best results if the source slits illuminated a small patch of sample centered on the goniometer axis, while detector slits admitted only photons coming from that small patch under observation. In real diffractometers we cannot expect these two areas to coincide with each other or the goniometer axis.