I'm talking about IEC motors-gearbox alignment. Here are an example:

Bell housings are often fixed with bolts or studs, these are convenient and take the required loads but do not generally provide adequate precision in location. Threaded fasteners really need a certain amount of clearance otherwise there is a significant risk of damaging the threads or the through hole during assembly or at least making assembly much more difficult.

Instead additional matching sets of features will be machined onto both mating parts which are designed to provide alignment to the required tolerances. In some cases fine adjustment may be provided by shims or eccentric pins etc.

A fairly generic method is to use dowel pins, unlike bolts or studs, which generally require a certain amount of clearance to avoid damaging the threads these will be machined with a slight interference fit.

Other options include machining matching rings, steps or tapers onto both parts. Taper fits tend to be especially good at ensuring concentrically on standardised parts as they tend to be self aligning.

In some cases final machining with be carried out with both parts assembled together making them essentially a matched pair. This tends to give the best possible accuracy but makes parts non-interchangeable.