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As Tex2002ans said, calibre cannot automagically fix badly-coded HTML. In fact, by default it doesn't try to fix it at all, other than flattening CSS and e.g. normalizing font sizes and line spacing.
Colors are the fault of the input HTML, certainly.
As for MHT, it may have been convenient for you in the past, when you wanted to save webpages for later viewing in Internet Explorer, but now you are learning why it isn't convenient as a general principle.
MHT is Microsoft's custom internal solution. Fortunately, it appears someone else was equally bothered by that lack of foresight, and created the application Tex2002ans referenced above.
Of course, it still won't save you from badly-coded webpages. ePubPress likely has a lot of code on their server devoted to cleaning up common badly-formed HTML, much like Pocket, Readability, Instapaper, etc.
That is outside of calibre's intended functionality.
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