Thanks for the suggestion. We are currently experimenting with a new CMake-based embedded project subsystem that is more flexible than the existing MSBuild-based one, and will try to include support for target-specific configuration for embedded frameworks in it.
As a short-term workaround, please consider cloning the Fixed Stack-Heap framework and placing it under %LOCALAPPDATA%\VisualGDB\EmbeddedEFPs under a new ID/name (see how the profiler framework is defined for a quick example). Then you can remove FIXED_STACK_SIZE=$$com.sysprogs.bspoptions.stackheap.stacksize$$ from the AdditionalPreprocessorMacros element and instead define it via regular per-configuration project properties.