The technical answer is because you have both an "Add to the global assembly cache ..." option checked and the Destination location option set on the Resource's properties in BizTalk Administrator.
The first puts a copy in the GAC. The second puts a copy in the install folder.
If you don't want the copy in the install folder, set Destination location to blank.
Why does it default this way? It's pretty much a standard .Net practice. BizTalk itself installed a lot of assemblies on both Program Files and the GAC. Some though are GAC only, I don't know the exact reason.