If it is NOT a linux native interface, it is NOT an analog of 'mono'.
Mono is available on many platforms, including Windows. What we have is a fork/package of Mono that is built for Windows and only used by Wine's internals. If Mono is "contaminated" then our package is just as much so.
On Windows, mscoree.dll is the interface that programs use to access the .NET runtime. However, the .NET runtimes are separate; mscoree is only the interface to them. We have an implementation of mscoree.dll in Wine, and our implementation uses Mono (which is in the wine-mono package) as its .NET runtime. The interface that mscoree uses to access Mono is the Mono embedding API. While the package also contains some other things that are specific to .NET, the core of it is Mono.