Functional modularity will remain a hypothetical construct, supported or not by molar behavioral evidence, for the foreseeable future. But science trades in hypothetical constructs. What bothers is when EP treats the brain as a hypothetical construct.
Brains really exist and have been studied for quite some time.
Networks and hierarchies. This has been well modelled by recent work by Kauffman on computational patches, and has been a standard part of theoretical biology thinking for many years. And further constraints lead to hierarchies - networks of networks. But these are not modules in the compartmented sense of computer science. They are dynamic entities - developed and stabilised by the functions they are called upon to execute.