That section describes the authority of Congress over what would become Washington DC, not what the federal government could use eminent domain as a tool for in executing its enumerated powers.
I don’t see eminent domain listed anywhere in the Constitution, though it does seem to be implied by the fifth (not that, IMO, that is enough to justify it).
Hmmm... looks like you are right, but then, there's
To make all Laws which shall be necessary and proper for carrying into Execution the foregoing Powers, and all other Powers vested by this Constitution in the Government of the United States, or in any Department or Officer thereof.
Which certainly includes buying land for the purpose of national defense, but not for transportation, other than perhaps the post office. BTW, getting rid of the post office and "post roads" is one instance in which I think an Amendment is advisable.