If this were a right that may be waived by the defendant, the venue would be okay. But it's not. It seems that the clause states that the trial must be held in the state of the alleged crime whether the defense and/or prosecution like it or not. Since this deviation was approved by both sides, no one has standing to challenge this.
I don't think there is a general standing problem with subjecting Article III's venue provision to litigation. Certainly there have been cases where the defendant requested an out-of-state transfer and the government opposed it. So the venue provision is not one of those issues that could never get challenged because of standing problems.
In the Oklahoma City case itself, I don't think the transfer was "approved by both sides." The government wanted the transfer to go in-state to Tulsa, but the trial judge found that the defendant could not obtain a fair and impartial trial anywhere in the state (decision linked below).
And as to the merits of the issue--whether it's constitutional to ever transfer a criminal case out of state--the reasoning seems to be that the Sixth Amendment's guarantee of an impartial jury and the Fifth Amendment's Due Process clause can conflict with Article III's venue provision in certain cases, in which case Article III has to give way.
The trial court in the Oklahoma City case wrote
: "The Due Process Clause of the Fifth Amendment of the United States Constitution requires fundamental fairness in the prosecution of federal crimes. The right to an impartial jury in the Sixth Amendment and the fundamental fairness requirement of the Due Process clause will override the place of trial provisions in both Article III and the Sixth Amendment in extraordinary cases. That is the foundation for Fed. R. Crim P. 21 (a) providing for a change of venue to protect from prejudice."
It's also not clear to me whether venue provisions are not subject to waiver. Appellate courts seem to have decided
that the right to venue is a personal privilege and can be waived. But regardless of whether one agrees with that conclusion, standing didn't pose a problem in litigating it (since the courts have obviously gotten around to deciding it).