After significant research, trial and error, and contacts to ESRI, it would appear as if the web applications created with web app builder do not print to scale. The reason for this is WGS 84 Aux Sphere projection used by the basemap is designed to preserve direction and shape but distorts distance and area. For some of our operations we need to be able to print to a specific scale and currently cannot do so. Has anyone else run across this issue, and have you found a solution that works for you?
You can create you own web map that use a state plane coordinate system as the basemap and then you will not have that issue. All coordinate systems have their trade off as far as distortion and you have to choose which spatial reference suits your needs and live with the fact that there will be less options for esri provided basemaps if you can not live with Web Mercator which Google, Bing and Esri use for their global audience.
Example: We want a 1” = 40’ print out
40’ * 12”/1’ = 480’
Take that number 480 and multiply it by 1.25 and enter that number 600 into the Print Widget’s Advanced dialog
Using a basemap and data in the web map using local state plane coordinates did not solve the problem for me. It seems like a bug in the print widget. I have an open ticket with ESRI Support on this.