Presumably those arguments in Eduyos were contemporaries. (Though not conclusive):
1). Beis Hillel and Beis Shammai span generations themselves (which somewhat invalidates the question, how can we know if beis hillel and beis shammai argued as contemporaries unless a Maaseh is written - however we understand their arguments continuing).
2). Either the Machlokes is resolved like Ben Butti (תלמוד ירושלמי מסכת חגיגה פרק ב דף עח) who was Beis Shammai paskening like Beis Hillel or it endures.
3). If an opinion is altered or retracted before the completion of the Mishnah, the Mishnah will hint to it. See Chagiga 2a-2b where the word כל comes to include a half-slave against Beis Hillel (even though his opinion is mentioned in the mishnah) hinting at the retraction.
4). Therefore, If there is a 3rd opinion without the above conditions it is a contemporary opinion. Furthermore, it is hard to imagine a 3rd opinion not being a contemporary if a בת קול states the Halacha is like Beis Hillel. Presumably an acceptance of Beis Hillel in the argument occurs; how could a 3rd opinion now come along 50 years later when we already understand כלל ישראל paskening like Beis Hillel until then.