ArcGIS QuickCapture will store your XY coordinates in whatever spatial reference is set in your layer. For example, if your feature layer is using a projected coordinate system, ArcGIS QuickCapture will store your geometries in that projection. If your feature layer uses EPSG:4326, all geometries will go with that...
The Latitude and Longitude device variables allow you to ALSO store the Lat / Lon values as GIS attributes in your layer.
If your layer is on lat/lon and you want to extract the XY values in a projected coordinate system of your choice, you can use the Project tool. This Esri Tech Support article may also be of help: https://support.esri.com/en/technical-article/000028012
Hope it helps.
