Yes, you're correct in noticing this ;) For some reason, WTP changed it so that server id and name are always the same now. This is, of course, a bit problematic.
As for seeing a request for name twice, this reason was also a WTP change in some part. They added a naming box to the first page of the wizard, but due to a bug, they didn't let the server adapter (ie, jbosstools) to set the default name properly.
Before this they didn't have a box on the first page asking for a name, and so we had one on our own new server page. Then they added it to the front page but did it incorrectly.
The bug ID for this is: