AFAIK, in certain states IRAs that originate from 401ks receive additional protection from creditors. That extra protection would be lost if such an IRA were combined with one from a non-401k source.
This may not matter to you but ... if you invest in brokered CDs and you do Roth conversions then ... Vanguard will not allow you to Roth convert a CD, only the entire IRA account. So, that could be one reason to not combine accounts. Fidelity, by the way, allows you to Roth convert a CD and even part of a CD.