Market does a few things that third party applications can't do -- most notable is being able to install apps without going through the permission screen (allowing it to verify permissions before downloading the app).
This is not a matter of signing -- Market is signed with Google's cert, not with a device's cert. The special things it does are features available to apps that are bundled as part of the system image. If Market were made available as a third party app, it would not be able to do these things. Likewise a third party app that is included by a manufacturer in their system image will have access to some additional functionality by virtue of being there.
Historically Market has also used a number of private APIs, which it could live with because it is always bundled with the device, so if one of those APIs changes the manufacturer will just need to make sure that they fix that to be able to run Market. Over time we have been cleaning that up to have it use many fewer private APIs.