Currently the MITK_RUNTIME_PATH variable (that is used to indicate the search paths for shared libraries (on windows only?) is compiled by ignoring extension pathes.
The logic to compile MITK_RUNTIME_PATH is encoded in mitkFunctionGetLibrarySearchPaths.cmake. Here any known EP gets his/her handcrafted treat. EPs from extensions are completly ignored.
Therefore extensions are not able to influence MITK_RUNTIME_PATH. This is e.g. a problem where an EP of an extension is generated externaly and therfore its libs are not in the default ep/libs folder.