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Sure you can use BAPIs in composite applications. And as a matter of fact you should use them as much as possible. Whether you can use the existing ones or you have to develop wrapper functions to them or create brand new ones, do it. And the beauty of BAPIs is that they can also be consumed via the Web service protocol in case the external program or system cannot communicate via RFC. No additional development effort is required to make a Web service enable the BAPI. SAP provides as of 4.7 or Basis 6.30 a generic Web service interface to all BAPIs or RFC enabled function modules.
RFCs are just function modules with the attribute "Remote function enabled." A function module without such attributes could not be consumed by external programs or systems using the RFC protocols. It would only be available within the system where it exists.
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