The derasha in Bemidbar Rabba (which is indeed "thought to be considerably later") includes the derivation from the verse in Divrei Hayamim, which would serve as a check from the name shifting. Meanwhile, the statement in Bava Batra does not include a derivation from a pasuk, and indeed, some commentators (such as Shteinsaltz) take the Talmudic statement which follows,
למאי נפקא מינה לתשובת המינים
to mean:
It is important with regard to an answer for heretics who inquire into the names of these women, which are not stated in the Bible. One can reply that there is a tradition handed down concerning their names.
Lack of an explicit verse means that the seemingly meaningless name, passed in tradition orally and then textually, could slightly shift.
Examining manuscripts of the gemara on the Hachi Garsinan website, I found that most agree with our printed Vilna Shas with צללפונית - namely, the Venice, Pizaro, Hamburg, Paris, and Escorial all have this reading.
In the Munich manuscript, they have צלולפוני with a final mark over the last letters, which would indicate a final ת but still is closer to the name as it appears in the verse in Divrei Hayamim. All you need is a scribe to assume that there should be an apostrophe there and it can get inserted.
Further, in the Vatican manuscript, we have הצללפונית, which has the initial ה though also unfortunately the final ת. Here is a picture of this:
