I see your point .. setting a typeface involves decisions re. kerning and many fonts use 'hinting' to ensure they can be read well at varying sizes, and some display faces are altered to suit headline text or specific use cases - but I think most logos have aims which are more specific than a typeface.
If people are free to alter the colours of a logo to suit a design, and the rules for doing so aren't defining clearly - before long a logo isn't able to fulfil it's purpose, because the unifying elements of the design become unclear.
That's not to say that a logo has to be the same everywhere - a successful identity system can break the rules, but if it does so, it needs to be very consistent in the way those rules are broken. I think agencies like Wolf Olins provide a good example of this kind of thinking.
I don't think the the adaptation of the HTML5 logo for the smaller favicon format is a feature - it seems like an afterthought.