Personally I don't find it confusing because it will look under whatever the current oozie config directory is. So /etc/oozie/conf.mycluster/tomcat-deployment would be used in this case. I wouldn't be opposed to, say, making it a peer directory, if you think that would be less confusing. So for all the components, tomcat configuration would be copied from /etc/<component>/tomcat_deployment, and in Oozie's case that would an alternatives symlink just like /etc/<component>/conf. If people seem to find that more robust, I'll go ahead and implement / test that.
edit: Actually, the more I think about it the more I really like that - that solves the problem of existing configurations getting upgraded because it's a new directory entirely. If anybody has had to mess with the Tomcat configuration they're hosed anyway, and this way everybody would just inherit the default configuration unless they take further action.