The problem is that PlatformIO doesn't recognize the '~' as your home directory. Using "~/projectpath..." should work, but there is a bug.
If it gets fixed that would solve your problem.
lib_extra_dirs = ~/Documents/Arduino/libraries <------ doesn't work BUG
lib_extra_dirs = C:/Users/je/Documents/Arduino/libraries <----- finds the dir, but absolute PLEASE FIX