We just federated our server to portal and we have some clients accessing our mapping services through arcgis desktop. Now they cannot access the resources without being prompted for a password. I've tried it too with my personal laptop and get the same issues. I tried the fix that ArcGIS 10.6.1 provided in the help article
Use ArcGIS Desktop with your portal—Portal for ArcGIS (10.6) | ArcGIS Enterprise and found that the only way I could access these services was by having to create an account for them. Is that the case? Is there any other way for some who wants to access our webservices through ArcGIS desktop without having to create an account for them?