The spatial reference of a feature class is made up of the following: coordinate system, tolerance, resolution, and domain. What follows is an explanation of how the spatial reference is set when processing and creating new datasets, are set and how to control these properties.
The spatial reference used during processing and the spatial reference used when creating the output feature class are the same.
When the output of a geoprocessing tool is a feature class inside a feature dataset, the spatial reference properties of the feature dataset is used as processing and output spatial reference. The exception to this is the M Tolerance, Resolution and Domain. These can be altered using the relevant environments, for more detail on this see links below.
If the output is a standalone feature class (not inside a feature dataset) the spatial reference properties used during processing and set to the output is the same as the input feature class' spatial reference properties. These spatial reference properties can be modified (or overridden) by setting relevant geoprocessing environments. For more details on each click the links below.
Z & M awareness environments