The idea of introducing different configuration files was based on the logic that each product has its own features/limitations and with the help of product specific configuration files we can set the parameters before starting a run.

The driver script expects from the user to provide configuration file specific to the product eg. 
For PS , we use pstress-run.conf
For PXC, we use pstress-run-PXC80.conf 

Ideally we should use a different configuration file for MS eg. pstress-run-MS.conf. But, the reason we do not have it in the repository is because PS is a derivate of MS and functionality wise both works the same, so we just points the PSTRESS_BIN to "pstress-ms" and re-use the same configuration file pstress-run.conf

Another issue I see is for eg:
A user may wish to use the same source code to compile and generate binaries for all 3 products 
pstress-ms, pstress-ps and pstress-pxc and place it in the same src directory and based on configuration file use them to do the runs.

Creating a softlink during compilation would involve making changes in the cmake files which will mean that we cannot use the same code to generate binaries for different product at the same time as the new softlink would replace the previous binary.

IMHO I do not consider this is as a BUG.