I recently heard that the Ibn Ezra brings down a minority opinion that the pasukim talking about "laying with a man as you would a woman" are actually talking about androgynous people. The Ibn Ezra disagrees with that, but he cites it nonetheless.
Obviously, modern Jewish Orthodoxy rejects this viewpoint, but after hearing it, I can't help but question why that is the case.
I think you are misunderstanding what that opinion held. The text of Ibn Ezra is (to Lev 18:22):
ויאמר רב חננאל ז"ל, כי יש מי שיחדש בגופו כצורת בשר אשה וזה לא יתכן בתולדה. וי"א אנדרוגינוס. וכל הצער הזה בעבור היות משכבי אשה לשון רבים. ודברי יחיד שני משכבים. והנכון בעיני, כי המצוה כפשוטה. גם אנשי התושיה חייבו מיתה עליה והכתוב אחז דרך כבוד לאמר כמו לא תקרב, ואחר שהזכר נברא לעשות והנקבה להעשות, הזכיר הכתוב שלא תהפוך דברי השם, ויש משכב להוציא הזרע, על כן מלת משכבי לשון רבים, ואין ראוי להאריך.
The textual problem is that the verse prohibits lying with a man in משכבי אשה "the ways of lying with a woman", in the plural. This plural form of "ways" is understood in a number of places to refer to both vaginal and anal intercourse (Kiddushin 22b, Yevamot 6:1-2). In the case of male homosexual relations, there is no second "way", yet the verse said "ways". Rav Channanel is quoted as suggesting that men may sometimes develop female genitalia, but Ibn Ezra rejects this as impossible. He then quotes "some" who suggest that vaginal intercourse with an androgynous male is included in the prohibition and constitutes the second "way" (one opinion in the Talmud Yevamot 83b indeed learns this rule from this word, though we don't rule accordingly (Rambam Issurei Biah 1:15)). Ibn Ezra then suggests that the correct read is just that "ways" is not an improper word to use in context for various technical reasons, and there is no need to find a second "way" for the prohibition to happen.
Thus none of the quoted opinions dispute that regular homosexual intercourse is biblically prohibited.
[Edit for clarification: As DoubleAA mentioned, the interpretation is apparently presented incorrectly in the OP. The rejected interpretation mentioned by the Ibn Ezra merely suggests that relations between a male and a hermaphrodite are included in the scriptural prohibition, not to the exclusion of standard משכב זכר].
This interpretation that the Ibn Ezra mentions and rejects is an interpretation of the simple meaning (p'shat) of the verse (Vayikra 18:22). It is likely that the Ibn Ezra rejects this as the simple meaning of the verse because it's doesn't make sense in the context of Vayikra 20:13, which explicitly refers to two males.
Regardless, for halachic purposes, we are concerned with the exegesis of the verse, not the simple interpretation. Exegetically, the Talmud derives from the phrasing "ואיש אשר ישכב את-זכר" (Vayikra 20:13, "And a man who lies with a male...") that the violation involves a man engaging in relations with another male of any age (Sanhedrin 54a). The Talmud explains that the term זכר ("male") cannot be an exclusive reference to hermaphrodites (Chagiga 4a), even though this particular biblical prohibition applies not only to standard משכב זכר but also inclusively to a man copulating with a hermaphrodite (Y'vamos 82b).
"משכבי אשה" (Vayikra 20:13, "...the manners of lying with a woman...") is interpreted exegetically as a halachic comparison between ביאה כדרכה and ביאה שלא כדרכה for a woman. As far as simple interpretations of that expression in the context of the verse, see the Ibn Ezra (Vayikra 18:22) and Rashi (ibid., 20:13).
