In short the answer is YES and definitely, you'll need at least one configuration file per node and you need a powerful machine to do so as @s1monw said.
I've done something similar where I have 3 physical servers and each has 32-core with 256GB of RAM. These servers were given to me, I did not have the option to spec out the HW for deployment. My estimate per node is at least 64GB of RAM with 2-core minimum plus hard drives per node or instance. So with my servers, I can run 3 instances at most, leaving extra resources to the host.
Just like what @s1monw said, running ES in this kind of setup, you'll need to make sure the replicas are in other physical machines, not co-located. Another issue that you might run into is file i/o when 3 ES instances are competing to read/write its own index files. If you have a choice, do one instance per physical machine... if you don't, set it up and test out your workflow before putting into production.