Maybe they sent cp0 or a gorosei/Gk to manipulate him as a kid, who knows, Van Augur said the gov sends dozen spies/assassins against BB all the time.
"You have a twin brother, do that or we kill him"
"Poison Roger or we kill the entire crew"
"Do that or we reveal your real name on the bounty"
Or they just told him they’d kill him and Buggy, who knows.
It’s been a theory since that pannel of Roger and Shanks talking and Shanks crying. Maybe Roger just played along bcz they really wanted to kill Shanks.