When setting up header search paths in IntroJucer, they are relative to the IDE-specific Target Project Folder rather than the .jucer file. This means that changing the Target Project Folder would require changing every path in the header search paths of every configuration of every added exporter.
I do agree with this, the ‘Local JUCE Folder’ path is relative to the Introjucer project file, perhaps all includes should be? It would save a lot of “…/…/” in the extra include settings and as Vinn says this wouldn’t be affected by the “Target Project Folder”. It would however break everybody’s existing Introjucer projects without some cumbersome “if version < … update to new path system and rename all settings”.