There is no assumption, but several Bible versions use the word "Julia" which is clearly a feminine name, and so is Junia.

Two Greek manuscripts have "Julia" (clearly a woman's name) instead of "Junia(s)" in this verse. One is papyrus P46 of about the year 200 (this goes against your idea of not until after 300 AD). The other is the thirteenth-century minuscule manuscript catalogued as "6". "Julia" is also the reading in some Latin manuscripts, in one tradition of Coptic manuscripts and in Ethiopic manuscripts. Three Greek uncial manuscripts have the inverse substitution, ("Junia(s)" in place of "Julia") in verse Rom. 16:15. This raises the question whether the proximity of the two names, "Junia(s)" and "Julia", on the same page is the reason why, in both cases, a few scribes replaced one name with the other.

No record of the male name "Junias" has been discovered in extra-biblical Greek literature. Three clear occurrences of "Junia" have been found. While earlier searches for "Junias" in Latin also yielded no evidence, it is reported that "Junias" has been found as a Latin nickname or diminutive for the name "Junianas", which was not uncommon both in Greek and Latin.[2]

Among the early Church Fathers, the United Bible Societies The Greek New Testament only cites Jerome as having read the name "Julia" in verse 16:7 and Chrysostom as having understood the name as "Junia". Chrysostom wrote: "O how great is the devotion of this woman that she should be counted worthy of the appellation of apostle!"[3] Although among the Fathers, "an almost universal sense that this was a woman’s name surfaces — at least through the twelfth century, ... this must be couched tentatively because although at least seventeen fathers discuss the issue (see Fitzmyer’s commentary on Romans for the data), the majority of these are Latin fathers,"[4] and "Junia", but not "Junias", was a common enough name in Latin. It has even been claimed that the first known mention of Junia as a male is by Aegidus of Rome (1245-1316), though this ignores the evidence of the Greek manuscripts about how the name was actually interpreted at least from the ninth century onward.

Over a millennia later, the idea of Junia being male is a form of deception, whence it was never the case before.

In summary, most highly regarded scholars consider Junia a woman's name. To be in prison does not mean to be in prison in the same room, necessarily. She was a noted apostle among the apostles.

Be at peace in knowing this fact! And therefore, treat women respectfully in the Work for the Church as apostles, elders, and teachers.