When I asked Arturo Ramos about this in 2008, he answered me by e-mail and responded:

" Jose:
My suspicion is that Manuel de Leon was the first person in his family with that surname. His marriage document clearly describes him as a mestizo and since Josepha de Escobedo, I am pretty sure was of pure Spanish ancestry, that would make his father the indigenous person in the pair. It was not uncommon for indigenous people in the 17th century to have NO surnames AND "de la Cruz" was a very common assignment of a name in lieu of a surname for indigenous people.
It is likely that if he lived in Colotlan, which his marriage document says he did, and he was marrying the daughter of a rich Spanish family, that he was a Tlaxacaltec soldier or official and thus it was a political marriage (as many are and were). Therefore his family likely had a Nahuatl surname and his father was in the "transition" to a Spanish name and thus did not use one regularly enough for the priests to put it down...
To give you an idea of the names adopted by the Tlaxcaltecs (and some Tepehuan families as well). Some common Tlaxacaltec names from Colotlan include Romero, Flores, Rios (all nature referencing) and Covarrubias and Escobedo (names of two of the most powerful landed Spanish families in the region... thus emulating)."

I think that Arturo meant to say that it was Manuel de Leon's mother Catalina de Garibai who was of pure Spanish ancestry.

Joseph de Leon