There was great interest in this nomination precisely because Mr. Stefanini was unusually qualified for the position and there was no apparent reason to repudiate it. I think you are right, though, that none of the principals confirmed or denied any specific reason for the Vatican's refusal to accept him. There was widespread reporting about the nomination and about the Pope's personal role in rejecting it. There are many articles available online if you want to read the reporting about the nomination and the withdrawal. As far as I know, there have been no explanations advanced with respect to the Vatican rejection of the nomination that do not relate to Stefanini's sexuality.
Defenders of the Vatican said the decision did not reflect on Stefanini so much as on Hollande's perceived insult to the church by nominating him. Something similar can be asserted about Trump's nomination of Gingrich (if in fact it happens.)