Hi Did you get to the bottom of this? If not, have you considered this long-shot:
1. A Margaret Helsby married a John Buckley in 1865 in the next area to Gorton. Maybe they had two children: Mary and John.
2. Perhaps her husband then died and she had an affair with a Mr Simpson which led to Thomas being born. She gave him the surname of the father but provided her original surname as she was no longer married to John.
3. In 1881 she was staying with her mother and sister with her three children: John, Mary and Thomas. This could explain why there were two under age lodgers in the house. Perhaps she gave the name of Simpson to hide the fact that Thomas was born out of wedlock but it was transcribed as Thomson. She also claimed to be a lodger.
4. In 1901 she was therefore living with her two sons who were step brothers. The "in-law" bit could be due to the "out of wedlock" status.
OK, it's probably unlikely but no one else has tried.