I use Bamboo as a build server and currently build our matlab c++ library target using deploytool. Configuration is done in the deploytool gui as normal, then I just call a very simple matlab function containing this code as the build step on Bamboo:
!deploytool -build "path/to/your/deploytool/project/file.prj"
You would probably want to use the -package argument instead of -build. Package will make the installer which should bundle the mcr if you have selected to do so in the deploytool gui. Also, using the ! forces deploytool to be blocking, so execution waits for the library to be built. Useful for our purposes and build system logic.
I know you mentioned your group likes to use mcc, but since the deploytool .prj file is just an xml file describing all the options and files to include it would be simple enough to use this as your point of configuration management. I check the .prj file into our git repo as it's the contents of that file that really decide how the build system runs.
This seems perfectly consistent with using external text-based / repo / whatever build config management your group may want to use.