Create symbolic links in that folder to each of the library folders needed by the project. Create a folder (outside of your project) to use as a dummy sketchbook folder, with a nested libraries folder. If you are working on a system (OS and file system) that supports symbolic links, here is a work around that should work (not tested). It looks like specifying multiple folders for that entry would do the trick, but there is no way currently to pass that through from the extension configuration settings. The interesting entry is otherLibrariesFolders, which points ONLY to the libraries folder of the Arduino IDE specified sketchbook folder. vscode/arduino.json for the protect, go there and look at. However, if you have added an output path entry in. There does not seem to be a makefile (as such) saved where I could find it.
The entries in c_cpp_properties.json for includePath tell intellisense where to look. Currently there does not appear to be a way to do what you want.
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