Wyoming, the clause you cited (known as the "Enclave" clause, Art 1, Sec 8, clause 17) has nothing whatsoever to do with Federal Ownership of land, other than allowing the Federal Govt to basically negotiate with the states for one of several of them to surrender land to form the new national capital. It in no way restricted or inhibited the Federal Govt to secure land from places other than existing states, nor did it place limitations on that land/territories that were already under its control.
The Controlling Authority on the Federal Govt's ownership and usage of land is contained in Article 4, Section 3, clause 2: "The Congress shall have Power to dispose of and make all needful Rules and Regulations respecting the Territory or other Property belonging to the United States; and nothing in this Constitution shall be so construed as to Prejudice any Claims of the United States, or of any particular State."
Thus Congress is fully authorized to make such rules and regulations it wants in terms of land held by the United States (Federal) govt WITHOUT restriction. This means it can keep, grant, sale, set aside for public use, lease, etc. any lands to which it owns.
Here's some of the records reflecting the intentions of the Founding Fathers during the drafting of the Constitution. It's pretty clear that the intent was to allow the Federal Govt, even when allowing for the entrance of new states into the Union, that it was allowed to keep those portions of the land within those new state's borders as it saw fit.
http://press-pubs.uchicago.edu/founders/documents/a4_3_2s1.html
Here's a fairly thorough discussion of the matter:
http://www.law.umaryland.edu/marshall/crsreports/crsdocuments/RL34267_12032007.pdf