IMO, it depends on the engine and Mfg. The modern castings in most Japanese engines are pretty good and can be mis-matched with no problems. Older engines that use bushings instead of ball bearings cannot be mis-matched without line-boring and lapping in the bushings and shafts. With ball bearing engines, a ball bearing can stand a 'minor' mis-alignment without causing a problem. The base gasket surface must also be taken into consideration and must be milled evenly on some engines. Not all Mfg's will sell a single case half. Kawasaki will sell a single case half but I'm not sure who else will.
If you use a used case half, just make sure the base gasket surface is flat and even and any bushings are line-bored and lapped in.