Independently contracted to Vault-Tec would make no sense, in that Vault-Tec makes Vaults not research into Viruses.
The timeline only gives 10 months for someone to say "Make a Vault for research into this new FEV strain" and for someone to say "Ok we can risk the chance of a security breach by sending this research to people that have nothing to do with Virus Research." It also does not make sense for them to Build Mariposa for the sole purpose of All FEV research and then turn around and say "we need another place for this research."
The Virus in Fallout 3 would have been created in the ten months before the great war at Mariposa. This means Mariposa has the means to house and study it.
Who said they got Vault-Tec involved, they could've gotten people from West-Tek to bring the FEV and then put those same people in Vault 87.
Vault-Tec would just've known that the government wanted to make alittle adjustment to 87.
The government could've expected that Marisopa could've been comprimised so they decided to put the other facility as far away from Marisopa as possible, D.C. The researchers would be right there too!
EDIT- And the guy who said all research was moved to Marisopa might not in the 'need to know' about Vault 87.