It is hardly possible, given that in 1490 Cesare Borgia was only 15 years old and could hardly be the model for the Renaissance depiction of Christ who is universally shown as a grown man. The idea that there is a link between depictions Cesare and Christ likely stems from the fact that on the Veneto's portrait made in early 1500s (it bears the Borgia's name, so it is generally assumed that it portraits him) Cesare bears a passing resemblance to a traditional Byzantine depictions of Jesus.

Depictions of Jesus in late 15th century and onwards vary greatly, but if we assume that the 'traditional' image is actually the one that shares similarities with the image on the Shroud of Turin, then it is very unlikely that it has anything to do with Borgia family, as they tend to resemble Byzantine icons of Christos Pantokrator (Christ the Universal Ruler) created as early as in late antiquity (the oldest preserved such image is the 6th-century icon, now residing in St. Catherine monastery on Mt. Sinai. It also houses 12th-century iconostas, where Jesus shows facial features similar to ones we're discussing in this thread. We can also find a similar image in the anonymous German painting 'St. Veronica with the Holy Shroud' dated to 1420's.

Now, if anything, then the times of Cesare Borgia (1475-1507) bring us more and more varied depictions of Christ, at least partially due to the development of visual art styles in Europe and the raising popularity of ancient Greek and Roman legacy. Even the most famous pictures and frescoes show a significant diversity of the Christ's facial features, so it is hard to fathom that anyone could 'force' a particular method of depicting biblical characters on contemporary artists. Even the cursory look at Leonardo's 'Last Supper' and Mantegna's 'Christ as the Suffering Redeemer' (late 1490's), Buonarotti's 'Last Judgement' (started in 1534), Theotokopoulos' 'Christ Carrying the Cross' (1580), Vecelli's 'Ecce Homo' (1576) or 'Crucifiction' (1588) and Caravaggio's 'The Incredulity of St. Thomas' (1596) reveals that in the 16th century depictions of Christ were possibly more diverse than before.

Now, it is quite possible that the whole notion is based on false presumption that was applied retroactively (sometimes attributed to 'Celebrated Crimes' by Alexandre Dumas Sr., although the text doesn't mention such situation). When speaking of the Christ-Cesare link, 'Portrait of a Gentleman' by Altobello Melone is often invoked. The problem is, that we actually do not know whether or not this is a portrait of Rodrigo's son and it was most definitely was not painted from nature, as the earliest works of Melone are dated to few years after Cesare's untimely death. To complicate matters further, Dossi (almost the same age as Melone) painted two portraits of quite possibly one person with different facial hair, one simply called 'Portrait of a Man', the other titled 'Le Duc Vallentin', giving a good support to theory that the person described is indeed Cesare Borgia (Duke of Vallentinois was one of his titles). Dossi's and Melone's depictions are nothing alike, so it stands to reason that at least one of them does not reflect Cesare's face. So, if anything, it is entirely possible that Melone, having never met Cesare Borgia's in person, decided to give him facial features typical to that of Christ he was very familiar with.