Marcus Stanford was arrested at his home in Forreston, in the Adelaide Hills, early on Wednesday morning.
The 24-year-old flower farm labourer is due to fly to Sydney on Thursday where he will be charged with being an accessory after the fact to Ms Scott's murder in the NSW town of Leeton in April.
Police will allege accused killer Vincent Stanford sent material in the mail after Ms Scott's death to Marcus, who then disposed of it.
In handcuffs and wearing a Star Wars T-shirt, Marcus appeared in Mount Barker Magistrates Court on Wednesday where detectives applied for his extradition to NSW.
Asked if he knew anything about the warrant for his arrest, Stanford told the court he did not and indicated he had not spoken to a lawyer.
Asked if there was any reason why he should not return to Leeton, he said: "Never been there, so I wouldn't need to return".
It is believed he and his two house mates, backpackers working on farms, were hauled into a police station to be questioned after his twin's arrest on April 8.
School cleaner Vincent Stanford is accused of sexually assaulting Ms Scott, 26, before killing her on April 5 - six days before her wedding.
The English and drama teacher was last seen at her workplace - Leeton High School - where she was preparing lessons before her impending honeymoon.
Forreston locals say Marcus Stanford had been living in the town, about an hour northeast of Adelaide, for a while and rented a house on Jamieson St.
"He seemed perfectly normal to me, quite nice and a very well-mannered guy," one local said.
The Forreston resident said Vincent Stanford had visited his twin brother over New Year's Eve for a holiday. Stanford is accused of dumping Ms Scott's body in bushland at Cocoparra National Park, more than 70km from Leeton, and setting it on fire.
Her burned remains were found five days after she was last seen.
Vincent and Marcus were born in Tasmania before they moved to Holland, from where their mother came, and spent a majority of their childhood there.
It is believed Vincent, his mother and older brother, moved to Leeton abut 13 months before his arrest.
He is due to appear in Griffith Local Court via audio visual link in September.
Marcus is expected to appear in a Sydney court on Thursday.
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