In the end of Season 1 we got Homelander, Billy and his wife on the lawn in front of the house.
What happened next (talking specifically about 3 of them): why did Homelander bring Billy there and how did he get away?
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This already got addressed in the show. with the gaps being filled in with character logic.
Homelander is a complete psychopath, he loves tormenting people and for Butcher knowing that Becca was still alive but out of his reach would be worse then thinking she was dead.
That's why Homelander brought Butcher to his wife to show him that he holds all the cards and the Butcher can't do anything about it. And hat his entire crusade/life after Becca's disappearance was a lie.
Butcher got spared by Homelander because Becca made a deal with him, Becca still loved Butcher so she wanted him to survive and in exchange for this mercy she would allow Homelander to see his son without making any problems of it. Homelander was inclined to honor this deal because he knew this would only prolong Butchers suffering seeing this forced butcher to live a life on the run away from Becca while also knowing that Homelander can reach her.