So Microsoft's MSVC from Visual Studio 2019 doesn't support C99 (or later), but it does support C89 and some constructs from C99.
Is there an option for the GCC C-compiler (not C++-compiler) to use a standard that would guarantee that the source can also be compiled with MSVC? If it compiles with -std=iso9899:199409 -pedantic under GCC, can MSVC compile it?
Pretty much the only way to you can ensure it builds with MSVC and GCC is to build the code with both toolsets. In addition to language constructs, there are a number of differences in the handling of compiler-defined preprocessor symbols, differences in what the preprocessor can handle, etc.
Personally I've been doing a lot of work getting C++ code to build with MSVC and Clang, and I've hit many minor issues that have to be fixed to get things to build with both toolsets. The C/C++ language standards help make the code portable, but you still have to run it through more than one toolset to get it to build 'cleanly'.
If you want your code to be robustly portable you also should build it for multiple architectures.
For my GitHub libraries, I build for ARM, ARM64, x86, x64 on MSVC, VS 2015 Update 3/VS 2017/VS 2019, targeting Win32 desktop, UWP, and Xbox One. I also build with clang for Windows for x86 and x64. Each one finds slightly different issues, but the end result is a lot more portable.
Is there a reason you need to care if MSVC can compile it? GCC ("mingw") can target Windows PE object files with ABI compatible with MSVC, so users could build with that, or you could even ship them binary object files/library files to use so they don't need any tooling.
Policing your code base for compatibility with a known-broken/intentionally-broken compiler does not seem like a worthwhile activity unless you actually have reason to want to use that compiler, rather than just allowing users of that compiler to link with your code.
-std=c90..... - S.S. Anne