OK, again....
1) The Constitution says nothing about public domain, its structure or any limitations.
2) The ruling points out how Congress can restore copyrights on material that is in public domain. The limitation is that it can't result in perpetual copyrights.
3) Yet again, §514 of the URAA was designed to mitigate claims based on the Takings Clause. That was the point of the footnote you cited.
4) The Takings Clause was not discussed at all in
Eldred and barely in
Golan. Again, if your position was viewed as a likely option, at a minimum it's not a part of the petition or dissent in either of those cases.
By the way, you kind of have the Takings Clause a bit backward. The literal text says
"nor shall private property be taken for public use, without just compensation." (emphasis added) This was only recently (and controversially) extended to include the seizure of private property for private use that allegedly serves a public good. I'm not aware of any indication that the government cannot "seize" a public resource and privatize it, at least not based on the Takings Clause. I mean, is the government supposed to compensate the government for selling a slice of land it owns?
(Note: this doesn't seem to be part of the reasoning in this ruling; again, the ruling just says "§514 is sufficient to satisfy concerns in the Takings Clause." I presume all parties roughly agree with the SCOTUS' evaluation.)
The
Atlas Shrugged example does not apply, because it would involve removing Constitutionally protected ownership from the copyright holders (presumably Ayn Rand's estate). The lake seizure is also not applicable, because the state is acquiring property from an actual owner via eminent domain.
Congress is not seizing property that you own, precisely because
no one owns it any more. The public doesn't receive royalty payments on PD works; the public can't assign the right to distribute a public domain work to a specific organization; the public can't block or grant the right to make a work derivative of a PD work. Neither the Constitution nor Copyright Law stipulate that a work in "public domain" has had its ownership transferred; all it says is that "after x years, copyright expires, and the copyright holder loses all the protections."
Further, part of the idea is that these works
should have been protected all along, and was not because the US was not upholding its obligations to Berne. It's not that the works were once protected, and new protection was imposed; it's more like the government recognizing it had a responsibility all along to offer copyright protection. I.e. the SCOTUS is saying that with URAA/CTEA, Congress restored the copyrights to the proper owners.
Now, Congress
could accept your argument, and rewrite copyright laws such that a work cannot be removed from the public domain once it's entered, or that when a work enters public domain, ownership is in fact transferred. But those kinds of decisions lie with Congress, because the Constitution makes no such provisions.