While it is somewhat self serving to answer one's own question, I haven't had any better answers, so here we go:
While for several Messianic websites that quote this passage are not actually clear on why they quote it, it seems to me that they appear to be taking it literally. In other words, they are saying that all prophecies in the Tanach are Messianic in nature. For example, one site says: "The entire Bible points to the Messiah" and then claims: "Ancient Jewish thought concurs with this:" And references Sanhedrin 99.
However, the problem with this is that the context of there Talmud passage tells us a different story.
For example, the section right after says: "And Rabbi Ḥiyya bar Abba says that Rabbi Yoḥanan says: All of the prophets prophesied only with regard to penitents..."
So what is it? Is it that all prophets prophesied about penitents or about the messianic era?
And later it says: "And Rabbi Ḥiyya bar Abba says that Rabbi Yoḥanan says: All of the prophets prophesied their prophecies only with regard to one who marries his daughter to a Torah scholar, ..."
So what is it? Is it that all prophets prophesied about marriage or about the messianic era?
The reality is that a brief examination of the Talmud in context shows that it doesn't mean what they think it means.
Rather, the full context is: "Rabbi Ḥiyya bar Abba says that Rabbi Yoḥanan says: In their prophecies with regard to redemption and the end of days, all the prophets prophesied only about the messianic era, but with regard to the World-to-Come the reward is not quantifiable, as it states: “No eye has seen it, God, aside from You, Who will do for those who await Him” (Isaiah 64:3). The Gemara notes: And this statement disagrees with the opinion of Shmuel, as Shmuel says: The difference between this world and the messianic era is only with regard to servitude to foreign kingdoms alone, as they will leave Eretz Yisrael."
(Note, the following has added words for the context and is taken directly from: https://www.sefaria.org/Sanhedrin.99a.12?lang=bi )
So, this shows us that the context is referring specifically to prophecies that themselves are about redemption and addressing whether they are exclusively about the Messianic era or ALSO about the World to Come (of which there is a dispute).