I was informed toyota place varying amounts of the metal turbo gaskets between the turbo and Y piece to allow for this 3mm which is slightly variable.
for example people have noted 1 metal gasket on each side where another identical set-up will use 2 on each side.
is it possible this is the answer in your case?
I have seen a very similiar pipe advertised for $515 ceramic coated to suit 1J soarer.
Yours is a good cheap upgrade specially if it will fit a cars existing engine pipe which is what it looks designed to do.
good luck with the sale!