In this case logic trumps proximity, and sound trumps grammar.

One way to make this more clear would be:
"The last 4 bars of the scherzo, which may be interpreted as a free inversion of the previous scherzo passages, then present an ascending arpeggio in the left hand."

This construction is also possible:
"The last 4 bars of the scherzo then present an ascending arpeggio, which may be interpreted as a free inversion of the previous scherzo passages, in the left hand."

As you point out, it is absurd to consider that a hand could be an inversion of something, so it makes sense to parse "ascending arpeggio in the left hand" as the next viable antecedent for "which".

Give my regards to JPRameau.

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"Sometimes I sits and thinks, and sometimes I just sits." - Satchel Paige

LCouperin wrote:
According to the "rule", the antecedent is the closest person or thing, in this case "hand".

I think you should doubt your rule. I think the rule should be formulatated: Normally or in most cases it is the last noun, but that is only a thumb rule and simply not exact. To tell the truth I don't know a rule. I think you have to find the noun or noun group, the relative pronoun refers to, by using logic and not an imprecise rule.