Build Variables and Linker Resource Path Variables are separate things.
Linked Resource Path Variables are only to be used when linking source files.
Build Variables are to be used in your build properties (compiler options, post buid steps, etc). \
Technically they are not supposed to overlap. For example, you aren't supposed to be able to use Linked Resource Path Variables in your build properties just like Build Variables can't be used to link source files.
However, this separation caused confusion among people who didn't know the clear differences (to them it is just an environment variable of some sort that can be used everywhere). So we eventually set it up so that creating a Linked Resource Path Variable also applied it to the Build Variables. I can't remember when this happened - in CCSv6 for sure and some of the later v5 versions I think (maybe 5.5).
In 6.0.1 we will make it even clearer