So my end goal is to get a list of all zipcodes within my city boundary. What I am asking is, both layers start with the same projection, it shouldn't matter what that specific projection is, the list of zipcodes that fall within the boundary will be the same every time. If I do the clip with both layers in web mercator and then I do the clip with both layers in UTM zone, zipcode X, Y, and Z will always be within the boundary. Projection will stretch, shrink, and rotate my polygons depenidng on what I use, but a point within a polygon will always be within that polygon assuming that point and polygon start out with the same projection.