I think there might be a bit more than people realise - for example, the last company I worked for did primarily C++ Windows applications, but we had several third-party C libraries built in as well (Python, GDAL, proj, etc) which we needed to be able to build in VC++. Presumably this kind of use case is exactly the sort of thing which would prevent libraries like Python from moving on to use C99 features.
I definitely agree that it would be much better if MS just supported those few features, which frankly don't seem that hard in the scheme of things. Makes me think that they see some advantage to them in not supporting it, although I'm not sure what that'd actually be.
Yes, a few of the libraries I've been involved with do not want to allow C99 features into the codebase because of MSVC. This, IMO, is the main reason for wanting some C99 in MSVC -- to stop Windows from holding the rest of OSS hostage when it comes to more modern language features.
I definitely agree that it would be much better if MS just supported those few features, which frankly don't seem that hard in the scheme of things. Makes me think that they see some advantage to them in not supporting it, although I'm not sure what that'd actually be.