So I noticed a lot of similarities between the vault 87 super mutants and the commonwealth ones, first off is the obvious color of their skin and the notable degradation of intelligence but some commonwealth super mutants will talk about "no green stuff here" and share the same violent tendencies as the Vault 87 ones.
Now, we've known the Institute has knowledge of D.C. since Fallout 3 with Zimmer, Doctor Li comes from D.C. and has lived in a mutant-heavy area for awhile and the Institute had a FEV division started by Father. My theory is that while the birth of the Commonwealth Super Mutants is different I think the method of how they were created and the origin of the FEV virus are the same. What if the Institute acquired the FEV from Vault 87?
The Institute has teleporters, they have synth technology to use as foot soldiers against the mutants and they have the scientists to use the research so it's not that far-fetched of a theory.