MSBuild uses ..\Studio\XX.0\bin\rsvars.bat to set the environment and quite a few people seem to use MSBuild for many things ( I admit I never directly used it yet).
One task it is used for is installation of packages (like TMS Subscription Manager does for example) . And here comes the pitfall:
If you changed BDSCOMMONDIR (where Bpls, Dcps etc are saved in sub folders) in options this change is not reflected in rsvars.bat, it still uses the standard path.
As Uwe Raab mentioned in a comment on google+ – and I add this for clarification – Bpl’s, Dcp’s are stored in subfolders of BDSCOMMONDIR as defined on the library page for each platform. I just override BDSCOMMONDIR to move everything away from my C:\ drive and I would except from an IDE that a change in one place of environmental settings is reflected everywhere.
But this again might be „by contract“ or „by design“.</sarcasm off>