Yes you need to publish SD file to bypass the default SR which is web Mercator if you are using Pro or even arcgis.com UX.
The UX does not expose the targetSR param we support at publishing.
So you can use the portal Publish API directly without the UX and you should be able to override the default behavior and specify any target spatial reference as a publishing param.
Publishing param in portal can contain:
{
"name" : "<yourname>",
"targetSR" : { "wkid" : <>"}
}
You can check how the UX is publishing from arcgis.com UX (fiddler, etc.). It does call the portal publishing from your data source.
Thanks
Khaled