At some point they were given no other choice but to tell people he was a Beta. Alphonse had been only ten years old when he lost his body, just a year shy of having settled into a second gender to possibly fall into, so back then, telling the truth and saying his second gender had yet to show itself was acceptable. But by age eleven or twelve most people have a second gender, and in some rare cases some could be considered "late bloomers" and settle at thirteen. By the time he was fourteen, with still no real idea of how, if, and or when he would get his real body back and therefor be able to get a second gender, he was give no choice but to tell people he was a Beta.
His metal body couldn't produce a scent like a real body could, like an Alpha or an Omega, and a Beta naturally didn't have a scent, so telling people, or letting them simply think he was a Beta was the only option open to him.
Often people would be shocked when told he was a Beta, most figured he had a personality of an Omega. Most people really didn't care to much though, and Ed often told him not to worry to much about it, that they would get his body back, he would settle, and if he settled as something other than Beta they could say he was an extremely late bloomer and that they told people he was Beta because they honestly thought he was due to his lack of scent. It was as close to the truth as they would be able to get, Alphonse knew that, but none of it felt right to him.
He wished often that he could have a real body, or at the very least that he would have settled before the accident that took his body so he wouldn't have to lie. He hated lying. He hated having to tell half-truths and tall tales. But for the moment, he was given no choice but to do the thing he hated most.
With any luck, he often would find himself thinking when he was up alone late at night, when he did finally get his body back he actually would be a Beta, then the half-truths would be full-truths and he wouldn't feel so bad about the lies because some of the lies wouldn't be lies anymore.
But for now, he would simply have to understand that he had no choice but to lie, and wait, and hope he could make all the lies, or at least most of them, true one day when he got his body back.
Hey, so this is my first Fullmetal Alchemist story ever. Mostly it was to help me get back out of yet another writers block, but I hope you all liked it. Let me know what you think in a review, and let me know if you want me to try my hand at a longer, maybe even chapter story for an Omegaverse Fullmetal later on when I really get back into the groove of things. Anyway, thanks for reading!