WinUAE includes a lot of "unofficial" patches and features that are not found in the base UAE tree. Some are Windows specific, some not.
It's fair to say that although WinUAE is always based on the Linux UAE base, it is also more advanced than the Linux version in terms of features.
It's to be hoped that some of the features added to WinUAE will make into the next release of the official source tree, but it appears that interest in maintaining that could be waning.
Certainly anybody considering running UAE on their AmigaOne/Linux set-up won't be getting anything even close to what Windows users get with WinUAE.
(e.g. bsdsocket amulation and JIT are not parts of the official UAE source tree)
