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What you see is expected. The Intel compilers, as well as the Apple development tools, are typically installed in both /usr (for use from the command line) and /Developer (for use from Xcode). This was done to allow those who keep their Xcode development environment on removable/portable media to move their Xcode installation, including any installed Intel compilers, intact from one system to another. (In Mac OS X 10.5/Xcode 3.1, there were still a few issues with this; I think they have been fixed in 10.6/3.2.)
While it is possible to install only the Apple-supplied command line tools, I believe that if you install Xcode, you always have both the command-line tools and those in the Xcode directory tree.
The Intel developer tools (e.g., compilers, libraries) are currentlyinstalled both in /usr and the selected Xcode directory tree. (If you have more than one version of Xcode installed, simply install the Intel compiler multiple times, selecting a different Xcode directory tree each time.)
In a future major release of the Intel compilers for Mac OS X, you will be given the option to install just the command-line tools, just the Xcode-integrated tools or both.

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