I see. It is because the syntaxer (the intellisense engine) uses the script as a source of the ref assemblies but not the Npp config file. This does not affect intellisense for the GAC assembies (major objective of the def asms in the config) but does for non-GAC ones.
Would be nice if a future version of the plugin would support this.
Based on our email conversation:
Would be nice if a future version of the plugin would support this.