Hi Michael,
Have you tried creating custom layouts and tapping in to your local PrintingTools/GPServer?
I'm not sure if that will help or not, but that is how we are doing it, and our measurements on the PDFs look pretty good (although maybe not exact). I'm using out ArcGIS Server basemaps that are in Alaska Albers, which might be the reason why the scale bar looks ok. ??
Still can't get myself to switch to WMA....although we lose some of the benefits of switching between projections, i.e. can't necessarily use both. Although I could swear that it worked the other day on a new map, but my older map doesn't like it.
http://adfg.maps.arcgis.com/apps/OnePane/basicviewer/index.html?appid=9420d52542a44d1c9636eea00b08ad...
I'm not sure if that AGOL maps is actually using thr GPService templates (set it up a while back), but our internal JSAPI app is, if you do a print from the "make a custom map" link for one of the hunts
Alaska Hunting Maps by Species, Alaska Department of Fish and Game
Just in case this helps any, since know one else had responded yet. Also tagging the https://community.esri.com/groups/alaska-gis-users?sr=search&searchId=c2e69eac-b629-4b27-bbe0-c54653... geonet group.