Tough question to answer without knowing more about your business. but - in general, I would say the answer is yes. I have a customer constructing complex electrical facilities. They use GP manufacturing to manage the production of certain sub assemblies - and then Project Accounting to manage the construction and commissioning of the facility...including issuing manufactured sub assemblies, sun-contracted work, buying in sun contacted parts, issuing parts from stock, timesheets etc.
I wouldn't describe the GP Project Accounting module as incompatible with other modules. It interfaces where required, but project accounting in itself can be a complex process - so expert help with implementing the GP Project Accounting module is advised.
Ian.