Making a fat model in Symfony 2 - Composition or Inheritance and how to configure my model layer

It seems like a complexity of your project is the modularity requirement - application behavior must be extensible via bundles. I'm not familiar with Symfony 2 / Doctrine 2 but a typical DDD tactic is to try and make sure that domain entities such as Order and Customer are unaware of bundle configurations. In other words, surrounding services should not add bundle-specific behaviors to entities. Delegating the responsibility for bundle awareness to entities will make them too complex. Fabricating entity class hierarchies to support extensive behavior is also too complex. Instead, this extensibility should be managed by application services. An application service would determine which bundles are loaded and orchestrate the appropriate entities as a result.

Another strategic pattern to consider is bounded contexts. Is it possible to partition your application into bounded contexts which align with the modules? For example, to address the $order-getShippingMethods() method you can create two BCs, one where there is an order model that has a getShippingMethods() method and another without it. Having two models may seem like a violation of DRY but if the models represent different things (ie an order that has shipping data vs an order that doesn't) then nothing is actually repeated.