@mksd Your assumption is right about making the Ref App & Bahmni living side by side. It should work fine for all the existing modules developed till date. But eventually, we should arrive to a place where the work can be re-used by following a standard way of extending Bahmni. One suggestion could be to go by OWA (for client side) + OMOD (for server side) and be integrated it into OpenMRS. Interested to listen more approaches.
Regarding the appointment module, one of our customers had a requirement of Appointment Scheduling module and we just plugged-in what is available in openmrs world. It was developed in a way that expects those patient attributes to be available in the system.