This is "Call Me Dumbo" (1966) by Bob Shaw, first published in If, December 1966 (link to the issue at the Internet Archive) and collected in Tomorrow Lies in Ambush.
She has a difficult life looking after her white-picket homestead, trying to attend to her children, and manage her domestic duties.
Dumbo bustled around the cottage trying to quiet her mind with work. Morning sunlight streamed across the breakfast table, making it glow like an altar. She set out five dishes of hot porridge then went to fetch the children who were tumbling noisily in her flower garden. Once out in the peaceful, sun-filled air she felt a little better. Beyond the picket fence the grain fields which Carl tended so carefully rolled down to the river like unleashed bolts of yellow satin.
She is regularly abused by her husband, who treats her with unexplained disgust. He also insists that she takes daily medication to manage some kind of chronic mental health issue.
Carl abruptly stopped chewing and looked at her with bleak, unfriendly eyes. "You didn't take your medicine this week. Did you?"
She stops taking her medication, and finds out that she is being kept in a dissociative fantasy state far removed from actual reality. In fact, she is on a harsh alien world without hope of rescue. Her homestead is a scratched-together habitat from the remnants of the wrecked ship that brought her to the planet
Dumbo sat up in bed, knuckling her eyes fiercely. The ceiling was wrong. In place of the familiar white plaster was an expanse of riveted gray metal, more like part of a ship than a rural cottage. It was as though she had been moved into strange surroundings during the night but—she looked around—this was her room all right. All the simple items of furniture were in their usual places.
She walked to the window and looked out at the front garden, but it too was wrong.
The fence was still there, but now it was made of crude stakes and wire, and inside it there were no flowers. Her roses had been replaced by wormless clumps of dark green foliage.
It is revealed that "mother" was in fact a male officer on board the ship.
"Because," Dumbo said triumphantly. "I was the only woman on the ship."
"You!" Carl stepped back slowly, appalled.
"You wanted me to yourself."
"You'll pay for saying that, Dumbo." Carl raised his fist, then relaxed it deliberately, one finger at a time. "Listen to me—you never had a brother. There was nobody on this ship but you and me. We were in the thick of a tactical emergency, so we tried to take the ship to Lark IV by ourselves. The suit you were looking at when I came in was your own."
Dumbo looked at the stiffly leaning pressure skin with its black maw of a face and boldly stencilled nameplate.
"But..."
"That's right." Carl laughed softly. "Hello, Victor!"
This truth is revealed to the protagonist by her "husband", who is callous and reveals his plan that, since rescue is impossible, he has concentrated on trying to colonise the planet
"There we were on a completely empty world. A clean, fresh world, ideally suited for life—and there was nothing for us to do but grow old and die." Carl's voice grew louder. "And Carl could not allow that. It would have been a terrible wrong—because the only obstacle standing in the way of Life was a few ounces of redundant male flesh.
"I had everything that was needed—the organ bank was in good condition then. The individual power cells are failing now, and I'm discarding more and more units every week, but at that time I was able to produce a usable set of basic female organs and glands for you. One hypno session after the operations and a weekly shot of an LSD derivative took care of the rest.
"That's your illustrious background. How do you like it, mother?"
The story twists with the revelation that the "mother" character has destroyed the artificial womb technology, re-started her medication (to permit her to slip happily back in to her homestead fantasy perception state)
It was a distant multiple explosion.
"What was that?" His shocked eyes hunted across her face.
"That, darling, was your organ bank. I had no idea the grenades would make such a noise. I hope they haven't worried the children. I must see how they are." She paused at the door and looked back.
Carl was kneeling naked on the bed.
"Oh, yes," Dumbo said. "I musn't forget this."
She took the hypo gun from a pocket, fired the charge into her wrist and went out to the startled boys.
The only incorrect detail is that the gender reassignment surgery has already been done, but Carl has been artificially inseminating Dumbo, which with the organ bank destroyed he can no longer do.
