You are clearly confused so there is no need to open your paragraph with that sentence. He would pay back the £1200 because that is what he is overpaid. Do you think the government just banks the 'extra' deductions?What I’m confused about here is what you’re referring to? Why not just quite the bit of the post you’re talking about? Do you think he’ll have to pay back greater than they’ve paid him or something? Like you think that he’d have to pay back £1200 despite the deductions taken? In which case I’d suggest you‘re confused. See the above post from @HangTime too.
They can deduct it from his future pay or they could get him to pay back the excess net amount (i.e. the excess amount they paid him).
As the post you pointed to put quite eloquently:
It would be far, far simpler for all concerned for them to just 'underpay' you in future, this means all deductions are automatically calculated and everything nets off to zero for all parties.
This means the gross is deducted by the amount of the overpayment and then tax, NI and student loan will rebalance themselves.
As an aside, please stop trying to draw me into a bickering match otherwise I'll have to report your post.