Consolidate to multiple or single instance SQL Server on a VM with many third party vendor databases?
Obviously an opinion here, but...
Personally, I think separate instances is definitely the way to go.  We have several servers at my work like that.  You have so much more control of stuff, especially server related objects like linked servers, etc.  Being able to restart one instance and leave the others alone is a valuable benefit.  And you can upgrade each instance independently as the vendor allows