Has the Catholic Church ever canonized a trans-gender person with the full knowledge of his/her true gender identity?
The short answer seems to be no.
I know of no such case within the Catholic Church and I am unaware of of any possible process of canonization being reviewed in Rome.
The point in question about eunuchs has a possible exception in the person of St. Philip the Evangelist. It has to be clearly understood that Philip the Ethiopian was an eunuch prior to his baptism and baptism cleanses the soul of original sin and any actual sin committed during one’s lifetime.
Whether the eunuch Philip was a castrated male or was in fact born that way, Scriptures do not say.
Philip the Evangelist appears several times in the Acts of the Apostles. He was one of the Seven chosen to care for the poor of the Christian community in Jerusalem (Acts 6). He preached and reportedly performed miracles in Samaria, and met and baptised an Ethiopian man, a eunuch, on the road from Jerusalem to Gaza, traditionally marking the start of the Ethiopian Church (Acts 8:26-39). Later, Philip lived in Caesarea Maritima with his four daughters who prophesied, where he was visited by Paul the Apostle.
New Testament
Philip bore a Greek name. He is first mentioned in the Acts of the Apostles (6:5) as one of "Seven Deacons" who were chosen to attend to certain temporal affairs of the church in Jerusalem in consequence of the murmurings of the Hellenists against the Hebrews.
After the martyrdom of Stephen he went to "the city of Samaria", where he preached with much success, Simon Magus being one of his converts. He afterwards was told by an angel of the Lord to go to the road between Jerusalem and Gaza. There he instructed and baptized the Ethiopian eunuch; next he was "caught away" by the Spirit and "found at Azotus" (Ashdod); and then "passing through he preached in all the cities till he came to Caesarea" (Acts 8).
Here some years afterwards, according to Acts 21:8–9, where he is described as "the evangelist" (a term found again in the New Testament only in Ephesians 4:11; 2 Timothy 4:5), he entertained Paul the Apostle and his companion on their way to Jerusalem; at that time "he had four daughters, virgins, which did prophesy".
Tradition
"St Philip the Deacon" is commemorated on October 11 in the Eastern Orthodox Church, in the Roman Rite, the Lutheran Church–Missouri Synod, and in the Anglican communion including, for example, the U.S. Episcopal Church, and the Anglican Church of Southern Africa. Additionally, in the Eastern Orthodox Church, Philip is counted among the Seventy Apostles, and is referred to as a Protodeacon; this feast day is celebrated on January 4.
Another point could be seen in the person of the Church Father Origen. Although considered a Church Father, he is not recognized as a saint.
On of the reason for this, is that some believe that Origen castrated himself, albeit in order to be chaste.
So why is Origen considered a Church Father, but not a saint?
Origen was a great teacher, but he also had some non-Orthodox positions on Scripture and the faith in general. His teachings were specifically anathemitized by the Second Council of Constantinople in 1553, which inherently means you can't be a saint, since you are condemned, at least according to the Roman Catholic Church.
That said, he was also an ardent follower of Jesus, a prolific and influential teacher, and fighter of other heretics.
The only reason he didn't get martyred was because his mother hid his clothes to keep him from going out.
He literally castrated himself because he felt convicted by Scripture.
He wrote vigorously against the Gnostics and other heretics, and even spurned his patron who supported other heretics.
Why is Origen considered a Church Father, but not a saint?
The Church does not doubt Origen’s holiness. However the Church truly frowns on self mutilation, whatever the reason may be.
In essence any Catholic could possibly be canonized, especially if one were martyred for the faith, that would include transgendered individuals, hermaphrodite individuals and eunuchs. Just like any other cause of beatification and or canonization, Rome would have to investigate their lives in order to see if the proper criteria of holiness and/or martyrdom could be met.
No offence is intended here. This is simply the Catholic position on this subject matter.
