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The parameter list of CSSMin::Remap allows for the option $embed with which you can set if the embedding of images has to be done. Currently the $embed variable is overwritten at position 150 ($embed = $match['embed'][0];).

Suggestion:
Change the function params to this:
public static function remap( $source, $local, $remote, $embed_data = true )

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and at line 159-160, change:
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// Embedding requires a bit of extra processing, so let's skip that if we can
if ( $embed ) {

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to:
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// Embedding requires a bit of extra processing, so let's skip that if we can
if ( $embed_data && $embed ) {

This way, even if CSSMin finds /* @embed */ comments it can be overwritten for performance/size reasons.