The Supreme Court has a long history of ignoring both the letter and the spirit of the law for the sake of politics and practical expediency. I can legally buy an AK-47 but not a Patriot missile despite the fact that the second amendment makes no distinction between different kinds of armaments. Allowing Patriots to be banned but not AK-47s is a distinction that the Court invented out of whole cloth. Likewise the weakening of the fourth amendment at the border is an exception that the Court invented out of whole cloth. Both of these exceptions were invented for defensible reasons. I don't want people to be able to buy Patriot missiles or nuclear bombs (or AK-47s). But that doesn't change the fact that there is a line that was invented by the Court out of whole cloth.
The problem is that the Constitution is broken, and has been since it was drafted. The right to bear arms probably should be conditioned on something more clear than the necessity of a well regulated militia (whatever the hell that means) to the security of a free state. The requirements for warrants probably ought to be weakened somewhat at border crossings. But the plain text of the Constitution does not allow this. The plain text contains no exceptions, and does not empower Congress to make exceptions. But changing the Constitution is hard, so rather than go through this slow, arduous process, everyone just punts the problem to the Court and says, "You deal with it." And so they do. The Court just does end-runs around the Constitution for defensible and practical reasons. But this doesn't change the fact that it is doing end-runs around the Constitution.