In The Syntactic Phenomena of English, McCawley considers the phrase “a dark blue necktie”, and concludes that “blue” in that phrase is simultaneously a noun and an adjective. It modifies the noun necktie, so it must be an adjective, but it must be a noun also, since it is modified by the adjective “dark”. If “dark” modified an adjective “blue”, it would have to be an adverb “darkly”, since adjectives can’t modify other adjectives.
But a skeptic might wonder whether “dark” actually does modify “blue”. Maybe, instead, “dark” modifies “blue necktie”, and we are simply dealing here with a noun “necktie” modified by the two adjectives “blue” and “dark”. The problem with the example arises because a necktie colored dark blue will always be dark, itself.
So let’s look for a less equivocal example. A “dark polka dot necktie” might have dark polka dots yet still fail to be dark, because although each individual polka dot was dark, if the polka dots were small and on a light background, the polka dot tie as a whole might be light, rather than dark. In that case, “dark” cannot be modifying “polka dot tie”, so it would have to modify only “polka dot”.
So, if a dark polka dot tie is not necessarily dark, then McCawley’s analysis must be right. Is it?
Putting to one side the parts of speech which may be involved, the OP is asking whether there is ambiguity (and how it might be made clear).
The two phrases under discussion – a dark blue necktie and a black polka dot dress have a clear, implied sense to me as British English speaker:
the necktie is dark blue in colour and the dress has black polka dots. Any other interpretation can be given easily by reordering the words, for example:
a blue dark necktie; a polka dot black dress.
The oddness of these two versions suggests that interpretations other than the (obvious) implied sense are wrong. In the first phrase ‘dark’ must qualify ‘blue’ – how can a blue necktie be dark except because its blue colour is a dark blue? The second version of the polka dot dress makes clear that this phrase is deliberately ambiguous. Only one colour is given but, clearly, another colour should be included since the dress background and the polka dots cannot both be black.
Instead of using word order – the idiomatic approach to conveying meaning – there is always punctuation:
a dark, blue necktie; a black, polka dot dress (making clear that the polka dots are a colour other than black).