According to Rabbi Refael Binyamin Posen in his book Parshegen (פרשגן) on Onkelos (Bamidbar, pp. 665-667 and nn.), the best manuscripts of Onkelos don't have the Aramaic of verse 3. It seems that this Aramaic list of names originated in one manuscript tradition of Targum Yerushalmi, and at one point some scribes mixed in this translation into some manuscript copies of Onkelos, and from there it made its way to the Onkelos of the editio princeps (first printed edition) of Mikraot Gedolot. In other words, Onkelos was consistent, but later scribes botched up some branches of the textual tradition and unfortunately these were used for Mikraot Gedolot, which is how this version of Onkelos was popularized and why this translation is thought to be original. It should also be noted that there are several variants to this list in other manuscripts of Targum Yerushalmi, including some significant changes.1
Per Rabbi Posen, I'll also correct my comment on the question: It's not entirely certain that these Aramaic names are Roman-era identifications of these Tanachic sites, because some of the names are literal translations of the Hebrew. For example, another version of the Targum Yerushalmi translates יעזר as סיען (Si'an); in Hebrew the word סיוע means עזרה (Ezra: help, assist). Nevo actually appears as-is in later sources, so the name בית קבורתא דמושה (the burial of Moshe) simply comes to explain the significance of the site and was likely not the actual name of the Roman period town at the site. Rabbi Yehoshua Falk (or Valk) in his commentary Beit Yisrael (AKA Perisha and Derisha) on the Tur, Hilchot Shabbat, § 285 also explained the name מכללתא as a literal translation of עטרות, because עטרה (Atarah) means crown, and מכללתא in his opinion comes from כליל (Kelil), which also means crown. On the other hand, בית נימרה/נימרין is known from contemporary sources (including being Yerushalmi Shevi'it 9:2's proposed identification of Nimrah). And כומרין in particular caught my eye because of its phonetic similarity to Qumran, and it has been suggested in the past that Qumran is derived from כומריא (Kumria, which means "priests" in Syriac (also related to כומר [komer] in Hebrew). While the general area of Ya'azer is far from Qumran, in light of the phonetic and possible etymological similarity, it's possible that there is a preservation of a real site name here.
1 For a full list of variants, see Alexander Sperber, כתבי הקדש בארמית, vol. 1, p. 279, verse 32. Can be found on Otzar Hachochmah.
