A priori, no. The safest solution is to assume that all of the compiler options are identical, except when the compiler specifically documents that the option doesn’t affect binary compatibility. (Documentation which is sorely lacking in most compilers.) In practice, in the lack of documentation, it seems a safe bet that options which control warnings (-W... in g++) won’t affect binary compatibility, and that options which affect code generation (language level, etc.) might: g++ generally maintains compatibility across different levels of optimization, where as VC++ doesn’t.
Another real problem is defining preprocessor symbols in the command line. Again, the safest bet is that all of the defines be identical, but also again, some common sense is in order: one can hardly expect the standard library to have been compiled with preprocessor symbols which are used in your project (things like MYPROG_CONFIG_FILE_LOCATION, say). On the other hand, be aware that preprocessor definitions of _GLIBCXX_DEBUG and _GLIBCXX_DEBUG_PEDANTIC will affect binary compatibility (although g++ ensures that you will get a library version which works with them if you use them consistently).
With regards to your question: I would not expect to much impact on binary compatibility due to standard version, but it would hardly surprise me if the choice affects some pre-defined preprocessor symbols, in a way that would break binary compatibility in the library, much as if you’d compiled some of the modules with _GLIBCXX_DEBUG, and some without. It might work, but I wouldn’t count on it.