The Thomas of "Wayward Dreamer" probably hasn't been committed, given that he's a) a kid, and b) nowhere near as troubled as the other two versions. However, it's possible that he ended up paying a visit to one at some point when he was younger: maybe a relative of his was institutionalized, or maybe his father worked there as a doctor and brought young Thomas along for a visit - Gabby later incorporating some of the experience into the games she played with Thomas, hence the scene where one of Gabby's dolls is encountered sitting at a psychiatrist's desk. Or, perhaps Gabby herself was brought to the asylum in order to be treated for catatonia.
"Final Descent" Thomas probably hasn't been committed either, given that he's encountered recovering from the depression in his own house, so it's possible that the asylum scenes were just Thomas's interpretation of his wife's increasingly frustrated attempts to snap him out of his depression.
Thomas might have gotten over it as the two grew up and eventually married, but sometimes he relapse back into that thinking to where Gabby had to vocally remind him he never even had a sister. It might have been frequent enough that Gabby treats it as a minor annoyance.
- The house where you move around as child Thomas has two childrens' rooms, with a common bathroom inbetween. It's possible that while he was never formally adopted, Thomas was taken by Gabby's parents to live with them, or at least that he stayed with them so often they had a bedroom set up for him.
The path for the game is fairly linear for half of the story, and once you reach the branch, all of the decisions seem fairly miniscule. (For example, the decision that puts you into either Broken Dreams or Final Descent is a matter of falling off the ledge or going back inside the hospital.) This has led this troper to speculate that perhaps all three endings hold some truth to them.
Given the nature of the game, it's not a far stretch to assume that each ending could possibly be another nightmare, or that every single sequence of the game is a nightmare, with all three endings revealing the true nature of Thomas and Gabby's relationship.
- "Wayward Dreamer" Thomas is a child, and Gabby is his sister. This ending would come first of the three. Gabby and Thomas were siblings (with Thomas possibly being adopted into Gabby's family), and Thomas developed feelings for his sister. He was quite protective of her, even as a child, and this ending would start the descent into the more romantic aspects of their relationship.
- "Final Descent" Thomas is much older, and this ending establishes his relationship with Gabby as her husband. Thomas eventually mustered up the courage to tell Gabby that he loved her (as more than a sister), and she seemingly reciprocated these feelings. Sometime along the way, the two married. However, the two tried to have children, with most of the children either being born prematurely with birth defects or simply dying in utero. This has put a constant strain on Thomas's mind, and as such, he asked Gabby to pretend that they weren't related. That way, he could feel more confident trying to have a child. This symbolism fits into the aspect of the giant baby monsters that he faces, as well as the womb that Thomas ends up in near the end. During this ending, it implies that Thomas had been institutionalized, and the final shot solidifies why. The two had a daughter, named after Gabby, that had survived much longer than any of their other children had. They had had enough time to bond with her, but, unfortunately, due to the true relationship of her parents, she fell ill to a birth defect and died. Thomas took her death particularly close to home, and this was potentially the start of his descent into madness. This ties into the doll enemies (as they symbolize the relationship he never got to have with his daughter), as well as giving better context to the younger Gabby enemies you face (as well as the Gabby enemies you face throughout the game in general). (However, dependent on the ending path, some of the Gabby enemies might also be manifestations of Gabby as Thomas's sister.) Gabby noticed that he was starting to refuse to spend time with her, and she eventually decides to leave him, because she wants him to move on.
- "Broken Dreams" Thomas is the last in the sequence, with him having attempted suicide, to the dismay of Gabby. In this ending, the relationship between the two is never specified. Thomas is in a hospital, and the level leading to this ending has him falling off the edge of the land of the hospital, implying that he slipped over the edge and decided to attempt suicide. He was more than likely a client there, as the effect of his daughter's death had already taken its toll on his psyche. He faces other patients because he fears that he is just like one of them. He also faces an evil version of himself, because he sees himself as the reason why his daughter died and Gabby left him. All of these things finally take their toll, and he attempts to kill himself. Gabby's sobbing implies that she still cares about Thomas, although whether she is choosing to stay his sister or she still has romantic feelings for him is left up in the air.
Long story short, the relationship between Gabby and Thomas is preserved throughout all three endings of the game. The deformed babies Thomas faces are manifestations of the previous children they had lost, the dolls are manifestations of the relationship Thomas never got to have with his daughter, the younger Gabby enemies are manifestations of his daughter haunting him (or manifestations of his past relationship with his wife), the asylum patients are manifestations of Thomas's fear of going insane, and the Thomas doppelgangers are manifestations of his guilt over his daughter's death and his divorce/separation from his wife. The kiss on the cheek he gives Gabby in "Wayward Dreamer" symbolizes the start of his romantic feelings for her, the womb he ends up inside of in "Final Descent" is a delusion of Gabby's womb (as part of his guilt for the deaths of their previous children) and symbolizes the start of his descent into depression and madness, and his apparent suicide attempt is the only non-symbolic part of the endings (as he has literally become a depressed shell of a man, due to constantly fearing becoming a monster through insanity or letting Gabby down again).
