What are the expected differences between an assembly compiled on Windows with the .NET Framework MSBuild and on Linux with Mono's MSBuild?

The use case I am looking at is a cross-platform application, and I would like to build for both platforms on Linux, ideally having one build process that targets both platforms. When xbuild was part of mono, I would have expected there to be differences between the two, but now that MSBuild has been open sourced and appears to have been integrated into mono, I'm not so sure. Was the whole thing shoved into mono?

Also, I am aware that .NET Core is an option, but I'm curious about MSBuild.