He didn't say these problems are a "good thing" at all. He said externals in Emacs can be used elsewhere easily than Eclipse plugins, and that's the "good thing

He didn't say these problems are a "good thing" at all. He said externals in Emacs can be used elsewhere easily than Eclipse plugins, and that's the "good thing" (being decoupled, modular). Sometimes these problems are just a motivation, not a need, for using externals, and that's why he criticizes js2-mode and Semantic (as they're not externals). He's indeed talking about the Unix philosophy.