используя отражатель вы можете видеть, что он действительно использует Object.Equals.
public static void AreEqual<T>(T expected, T actual, string message, params object[] parameters)
{
if (!object.Equals(expected, actual))
{
string str;
if (((actual != null) && (expected != null)) && !actual.GetType().Equals(expected.GetType()))
{
str = (string) FrameworkMessages.AreEqualDifferentTypesFailMsg((message == null) ? string.Empty : ReplaceNulls(message), ReplaceNulls(expected), expected.GetType().FullName, ReplaceNulls(actual), actual.GetType().FullName);
}
else
{
str = (string) FrameworkMessages.AreEqualFailMsg((message == null) ? string.Empty : ReplaceNulls(message), ReplaceNulls(expected), ReplaceNulls(actual));
}
HandleFail("Assert.AreEqual", str, parameters);
}
}