Prior to Lateran IV nobody regarded the doctrine of transubstantiation as the official account of the real presence of Christ in the Eucharist, and even after Lateran IV nobody regarded it as heretical to suppose a different account of the miracle. Thomas Aquinas is in fact the minority report: he is the first to ever say that denial of transubstantiation is heretical, and after him we can find lots of open disagreement on this point from Scotus, Ockham and others.
More interestingly, what Scotus and other post-Lateran IV theologians consistently say is that while transubstantiation can’t be justified by plain meaning of the scripture, nor by reason, it is nonetheless true by virtue of the primacy of the Bishop of Rome, i.e. by ecclesiastical fiat, because the scripture is interpreted by the same spirit in which it was written and revelation is thus continuous. More plainly, it is the true explanation purely because the Church says it is.
Luther in fact takes this point up in total agreement with the majority report as exemplified by Scotus: his question is not whether or not transubstantiation is true, but rather whether its canonization as dogma can be a legitimate exercise of ecclesiastical authority — wether, that is, the Church can rightly demand credence to a doctrine which is neither obliged by scripture, nor recommended by reason, nor seems to make any difference at all to Catholic religous practice, as even the majority of authorities concede. His question is not so much unanswered as unnoticed as the debate derails into the question of whether transubstantiation is credible, rather than whether it can be properly made an article of faith.
At the Countil of Trent, something rather odd happens: a misreading of Lateran IV motivates a kind of fallacious stare decisis about a decision that was never in fact made. Lateran IV was concerned with securing the dogma of the real presence of Christ in the Eucharist against heresy and took transubstantiation as the best explanation of it, without actually going so far as to declare the alternatives heretical (or even consider them very rigorously). At Trent, we see theologians relying mostly on Lateran IV to argue for making transubstantiation canonical, which is circular reasoning not directly supported by the text in any case. Nonetheless, the consensus grows and becomes official, and Thomas belatedly goes from being a bit of a marginal thinker to defining the mainline of Catholic theology, largely because he provides the strongest cudgel with which to beat Protestants.
Moving forward a century, we find Descartes in the unusual position of trying to justify transubstantiation on non-Thomistic grounds, but in the process he refigures the doctrine so completely as to make it as unrecognizable to Thomas as Thomas would have been to Aristotle. Nonetheless, it does represent a credible account of the dogma of real presence, and its failure to find acceptance owes less to the intrinsic necessities of Christianity than to the aforementioned stare decesis — in other words, that it is entirely derivative on another point, never decisively settled, as to whether credo can be mandated by ecclesiastical fiat alone.
This all implies that what is taken to be a decisive point of Catholic dogma to this very day rests entirely on an unresolved and seemingly distinct argument, where transubstantiation is justified by appeal to the primacy of the Bishop of Rome, and the primacy of the Bishop of Rome is interpreted in such a way that this sort of ecclesiastical fiat is within his proper purview. This was precisely the point at issue in the Reformation, and remains an open question to this day; even Catholics like McCue can be found raising it as a question.
On the basis of the Patristic literature, McCue comes to the conclusion that the ecclesiastical primacy of the Bishop of Rome is justified entirely on the necessity of maintaining coherence within the Church. Though McCue does not say so, it is implied by this point of view that any demand which contributes to the incoherence and splintering of the Church cannot in fact be within the proper purview of the Papacy, and that fiat of the sort involved in the case of transubstantiation cannot properly result in a modification of dogma. In other words, Luther was right to ask the question and demand an answer, which he never got but could have if Trent had gone a different way.
This does not violate the dogma of the Primacy of Rome; it merely sets principled limits to what that dogma can mean, based on precedent found in the Patristic era. As a consequence, it means that the Pope can and should mandate a return to a minimalistic commitment to the Eucharist, not as requiring assent to transubstantiation — a doctrine whose motives are contingently but not intrinsically Catholic — but only the real presence of Christ, however we might understand it within the bounds of orthodoxy.
This would have the effect of removing one of the major barriers to reconversion back from Protestantism back to Catholicism, and of finally answering the central complaint that motivated the Reformation in the first place, by removing precisely what is objectionable to Christian conscience about the use of Papal authority and leaving everything else intact. As the doctrine of transubstantiation rests admittedly on nothing but ecclesiastical fiat, this fiat by the same logic can be impeccably revoked, and without doing any violence to other essential dogmas. It would not even require admission of error: merely a choice for the Church to undo by rights what she once did by rights, which would do nothing to undermine the basic faith of Catholics.
Roger Ariew, Descartes Among the Scholastics
James F. McCue, ‘The doctrine of transubstantiation from Berengar through Trent: The point at issue’
James F. McCue, ‘The Roman Primacy in the Second Century and the Problem of the Development of Dogma’
Stephen M. Nadler, ‘Arnauld, Descartes, and Transubstantiation’
Eric P. Lewis, ‘Descartes and Tradition: The Miracle of the Eucharist’