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I answer my own question about how penelope handles it: It doesn't even try to save some space by using the variant tag in cases where that's possible. Instead it just has a new word-definition-pair for each synonym, so that some definitions simply appear several times - this will blow up the dictionary significantly in certain cases (see penelope3.py, lines 1130-1132 and 1180-1197).
A really unfortunate dictionary format :-/
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