Although wine was initially written with the ability to use a full-blown windows install, it is a very bad idea to do so. Thus both registries will be separate.
Yet, depending on the software you run, it can actually work nonetheles.
If you install, say, a game on windows, then reinstall it in wine, at the same place, there are high chances the game will never update the registry past the installation, and data will be the same on both, everything will stay "in sync", so there's a very high chance that it will work (I've done it myself in the past).
But depending where the software configuration is stored it might cause problems. Both registries will be different, and filesystem is shared, so let's hope that system-dependent configuration (like graphics settings) is stored in the registry and independent stuff on disk (like key bindings).
You might run into trouble too if you try to update the application, and such an update applies a delta patch on files (vs overwriting) AND updates the registry with patch info. If so, you will have to do some file swap dance to patch on both. If it does only one or the other, you're clear.
Alternatively, there is another solution, also depending on the software run in wine.
You can use wine prefixes (by default WINEPREFIX=~/.wine) to tell wine where to store its data. Thus one can initialize independent "windows" instances. Everything wine needs WRT each instance is self-contained inside this prefix.
So it's perfectly possible to share this prefix between multiple non-concurrently running wine installations be they on the same OS, on two different computers (with the prefix being on a shared storage, like NFS), or on two dual-boot OSs sharing a partition.
I don't know what the current state of wine on windows is (yes, you can run wine on windows!), but if it works well you could indeed share the prefix between wine on linux and wine on windows.
The only part bothering me is os-specific things like the symlinks defining the drive letters inside the prefix, or the sound output config (stored in wine registry).
To sum all this up, it can work (and work really well), but it depends very much on the software you will run, and some little tricks and hackery (scripts, mount points, symlinks...) here and there might be just what's needed to make the software behave.