Yes, I noticed that there was a different URL, but unfortunately this is still up to VS 2010 and the "Publish" window to decide which url.
Apparently VS 2010 is really NOT ready for being used in conjunction with your tool.
Here a list of a few points that I believe being bugs in VS 2010 publish:
1. You are forced to use https
2. You are forced to finish the url with "msdeploy.axd"
3. It automatically transform your URL adding the querystring of your site (used for wmsvc for IIS 7.0) so it's not possible to use it with IIS 6.0
4. If it was meant only for iis 7 it should be stated somewhere.
I opened a thread on VS 2010 support forum which is still unanswered: http://social.msdn.microsoft.com/Forums/en-US/webdevelopmentprerelease/thread/99077ce1-a656-4054-a33c-41920ee9516c
It would be very appreciated if you liaise with that team to further integrate the deployment into the IDE.
Thanks