That's why residual vector quantization is a useful technique - using multiple dictionaries to quantize a single timeslice, each conditioned on the previous residual level. You can also quantize a signal at different frequencies.
There are samples towards the end of the post of their LLM trained on their Mimi audio codec.
I read the article and confess some of the modeling parts were above my comprehension. But I would like to add that as an audio engineer, the "key question" you describe is solved, just not applied to transformer models (?).
An experienced engineer can look at a waveform in a DAW and identify specific consonants, vowels, specific words, etc quite fluently. And with tools like Melodyne - which already quantize audio semantically - they can identify (and manipulate) pitch and formants as well, turning an O vowel into an E vowel, or changing the inflection of a phrase (up-speak vs down-speak, for example).
I don't know how to apply this to a neural codec, but it seems like it shouldn't be that hard (that's my naivete coming through)
DAWs' rendered waveforms have so little information that such identification is likely impossible even in theory. Telling apart plosives and vowels maybe, but not much more than that.
I work with phoneticians and they can (sometimes) read even words from suitably scaled spectrograms, but that's a lot more information than in waveforms.