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Now if this were a matter before the Supreme Court then shouldn't it be identified as such instead of being issued in the District court?

It was filed in the District Court, not decided or issued as a District Court decision.

The Chief Justice ordered the writ, his Supreme Court clerk issued it, but it eminates from the District of Maryland and is heard in the district court. It was not a Supreme Court ruling or a Supreme Court decision. Constitutionally the Supreme Court had appellate jurisdiction and not original jurisdiction. Taney can't bypass the circuit court just because he wants to. His actions in issuing the writ may well have been in his role as a Supreme Court justice, they have that power. But his ruling was performed in his role as a circuit court judge.

The 1863 document image I posted lists it as an at chambers decision of the Chief Justice of the United States, not a Circuit Court decision. This is consistent with the Hartnett and Farber references I provided. Hartnett argues the following:

At the conclusion of the proceedings before him, Chief Justice Taney ordered "all the proceedings in this case, with my opinion, to be filed and recorded in the circuit court of the United States for the District of Maryland," an order that scarcely would have been necessary if the proceedings actually had been conducted in that Circuit Court, but which may help to explain why the case frequently has been thought of as one before that Circuit Court.

And

Swisher, supra, at 847 (noting that "at that time and for many years thereafter opinions written at chambers were not usually printed in official reports"); id. at 849 n.26 (noting that although the Federal Cases citation to Merryman refers to the Circuit Court for the District of Maryland, this "is not to be taken as an admission on the part of the Chief Justice that the case was disposed of in that court" and that "[h]e continued to treat it as a decision by the Chief Justice at chambers").

Seems Taney got his decision on the printed record as an at chambers decision of the Chief Justice of the Supreme Court. Thank goodness he did. It is a profound well written document, and it would have been our loss if it had not been preserved.