At present Passenger uses 2.3.0, but most of the other scripts use the default Ruby which is 1.9.3.
The Ruby 2.x versions have many improvements and new features (e.g. __dir__ and to_h). It's likely that developers will be using a later version than 1.9.3. This makes it harder to test whether the code is compatible with that version without deploying it and seeing if it breaks... The simplest solution might be to link /usr/local/bin/ruby to ruby2.3.0. It looks like /usr/local/bin is on the PATH ahead of /usr/bin so that should just work. Might it be worth trying that?