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What is Output Coordinate System and does it matter?

I am using Pix4DMapper Discovery and have a Phantom 3 Pro.  When I import the images into Pix4DMapper the Coordinate System is auto detected as Datum: World Geodetic System 1984; Coordinate System: WGS 84 (egm96). 

When I go to select the output coordinate system it defaults to Datum: World Geodetic System 1984; Coordinate System: WGS 84 / UTM Zone 18N.  However if I change the Units from M to ft, it changes the coordinate system to Datum: North American Datum 1983; Coordinate System: NAD 1983 StatePlance New York Long Island FIPS 3104 Feet. 

I live in the US so feet is easier for me.  What does the output coordinate system do, and does it matter if I change it? 

Thanks.

The output coordinate system is the coordinate system that is used to store the spatial data of your final project. It won’t change the way that the project is visualized, but some coordinate systems are better for certain regions than others.

WGS84 is a global system, while NAD 83 is a regional system, which is designed for that specific region. Choose the system that is best for you depending on what you need or what your client needs.

WGS84 is defined in meters which is why it defaults to NAD83 when you change it to feet, which is the unit of measurement for NAD83.

If you’re not sure what system to choose might as well keep it as is.