Which Protestant theologian first clearly formulated the penal substitution theory of atonement?

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Hard to choose, but probably Martin Luther. Your linked answer has the clearest example, from Luther's Works, Volume 26 (Lectures on Galatians Ch. 1-4).

He sent His Son into the world, heaped all the sins of men upon Him, and said to Him: "Be Peter the denier; Paul the persecutor, blasphemer, and assaulter; David the adulterer; the sinner who ate the apple in Paradise; the thief on the cross. In short, be the person of all men. And see to it that You pay and make satisfaction for them....Whatever sins I, you, and all of us have committed or may commit in the future, they are as much Christ’s own as if He Himself had committed them.

However, this is from a 1535 lecture, and so it's not the earliest instance, per se.

In 1530, penal substitution was officially proclaimed as part of the Lutheran faith by the Augsburg Confession at the Diet of Ausburg. (Note the similar phrasing.)

Also they teach that men cannot be justified before God by their own strength, merits, or works, but are freely justified for Christ's sake, through faith, when they believe that they are received into favor, and that their sins are forgiven for Christ's sake, who, by His death, has made satisfaction for our sins.

Luther approved a draft of the confession, so it's likely that he supported this view of the of atonement by this time, if not earlier.

Around the same time, John Calvin wrote Institutes of the Christian Religion, which was published in 1536.

He offered in sacrifice the flesh which he took from us, that by expiation wought he might destroy our guilt and appease the Father's just anger.

It's hard to say who had the idea first. Given that Protestantism relied especially on Paul's works, and this interpretation is best supported by him ("For he hath made him to be sin for us"), it's not surprising that Protestant theologians arrived at this doctrine readily.

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