Given your response to my first answer, that certainly as a good reason to do such a thing. The answer is yes. If you put these differing configurations in the same app and that app is/was NOT deployed from the deployer, then it should be fine.
hmm, the thing is I want to implement SAML on the search head cluster. I am unable to create the same entityId for all the search heads in our IDP, so each entityId has to be different so the configs would be different for all the search heads. I was thinking to put the related in an app and deploy individually on the search heads, version 6.5,3