the referenced directory should work
as if it had actually been added to
%PATH%, right
No, if you had C:\bin added to your %PATH% and inside c:\bin you created a Junction called c:\bin\anotherDir\ to point to c:\anotherDir\ so that you could run some.exe from the command line like:
> anotherDir\some.exe
This would not work since the %PATH% variable does not work with sub directories (symlinked or not)
you would need to create a hardlink directly to some.exe, so the hardlink c:\bin\some.exe points to c:\anotherDir\some.exe
So in summary I don't believe you can do exactly what you are asking. That said I do recommend Link Shell Extension for creating Junctions and hardlinks. It offers more capabilities than most junction tools in a very easy to use windows explorer extension