Rather strange, Perne's actions in that year of 1564. I wish I knew more about the day-to-day changes in the direction of the winds which bore upon that Weathercock. I am no historian.
My uninformed suspicion is that 1564 was a time when the future of English Christianity either still hung, or was thought by some still to hang, in the balance. A recent book by John Guy has emphasised that the more murderous part of Elizabeth's reign did not start until around 1584; and the Handlist of the English Martyrs does not resume, after Henry VIII, until the aftermaths of the Northern Rebellion of 1569 and the Bull of Excommunication in 1570. The Missionary priests did not start to arrive until 1574 and John Gerard's autobiography explains how little interest the government took in the activities of Marian priests. 1564 was, after all, only five years after 1559.
As the Royal Visitation of Cambridge drew close in 1564, Edmund Grindal (who had spent the previous reign as a refugee in Strasbourg) was somehow mysteriously outmanoeuvred so as to be unable to prevent the nomination of Perne to preach the sermon. Significantly, Grindal distinguished between "dissemblers and neutralls", and "the zealowse and syncere". Perne, he believed, manifestly and disgracefully fell into the former category, and ought not to be given any encouragement.
So Perne preached eloquently on the Royal Supremacy (Romans 13:1). Eloquently and acceptably. Might he have been planning so to melt the wax in the Royal Ears that they might more graciously incline to his speech at the Disputation, later in the week, in which he set the authority of the Church above that of Scripture? Or was it that the royal favour was made so explicit to him that Perne, as he later hinted, improvised a speech which he had not originally prepared or intended? Collinson points out that "all the old popish guard, the unreconstructed Marian heads of houses, were drawn into the lists ... Apparently in the perception of Cambridge this, rather than the abortive disputation at Westminster Hall in 1559, was the crucial occasion when Protestantism might yet meet its intellectual nemesis". And Perne was cast in the role of Master Doctor Nemesis. A sort of Proto-Pusey?
Perhaps we should revive Grindal's phrase "Dissemblers and Neutralls", or "D-and-Ns", as a 'churchmanship category' when we try to analyse the convictions of an Elizabethan clergyman. It would be jolly to know how broad a category it was! It might not even presuppose that a cleric had been ordained during the use of the Latin Pontificals, since quite a number of the Catholic Martyrs had been previously in Anglican Orders; beginning with the Protomartyr of the Seminaries S Cuthbert Mayne (of St John's College).
In conclusion: another jolly enquiry for some keen youff or youffess might be the publication and acquisition dates of Perne's Patristic texts, combined with a careful reading of his annotations. What about testing a thesis something like this: "While the invention of Anglicanism largely rested upon a dislike of Calvinism and of Calvinists, it also owed a great deal to the dissemination of newly printed Patristic texts".