Not sure what you mean by the "mozilla thing". I think there are other issues involved besides optional plugins, but am hardly an expert.
All I can tell you is that ie4linux doesn't work the same (or at all for some sites) as the same version IE running under Windows, so that if you wanted to validate your site with IE under wine, you'd better run it under wine.
I haven't found any cases where IE works on a web site under Wine, but not under Windows, so if I were validating a site for IE, that is the lowest common IE denominator I would use.
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