This diagnostic (which defaults to an error, added in 95833f33bda6c92e746e0b0007b69c2c30bfc693) was (as far as I can see) intended to clearly point out cases where the C++ ABI won't match the Microsoft C++ ABI, for cases when this is enabled via a pragma over a region of code.
The MSVC compatible struct layout feature can also be enabled via a compiler option (-mms-bitfields). If enabled that way, one essentially can't compile any C++ code unless also building with -Wno-incompatible-ms-struct (which GCC doesn't support, and projects developed with GCC aren't setting).
For the MinGW target, it's expected that the C++ ABI won't match the MSVC one, if this option is used for getting the struct layout to match MSVC.