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Given that a cat has been cloned and the clone looks little like its clone (except insofar that both look like cats) I'd say that the determination of how genes operate is still very much a black box. Oh sure, we know about alternative splicing, siRNA, microRNAs, transcription factors, chromatid organization, recombination, etc., but getting from sequence to function is not [yet] fully characterized.
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We already knew from identical twin kittens that fur colour patches are largely randomly determined and cat breeders had also worked out that in some cases fur colour is also affected by the temperature the kitten is exposed to while young. So someone knowlegable about cat genetics wouldn't expect cloned cats to look the same.