"independence" here is meant in a mechanical sense, not in a statistical sense. For example, suppose we have a language with two lexical tones, high and low, and the lexicon just happens to have twice as many high tones as low tones on /i/ vowels, but half as many high tones as low tones on /u/ vowels. In a dataset of speech from such a language, there will be a statistical correlation between vowel frontness and f0. Source-filter theory does not attempt to account for these kinds of correlations. The mechanical sense of independence only means that the tongue, lips, velum, and jaw can move around without affecting glottal tension, and glottal tension can change without affecting the tongue, lips, velum, and jaw.