The module returns a list entities that is not ordered in any way.
Hence, when viewing the diff, if the order of the entities doesn't match, wrong entities are compared and a difference is shown.
This can be resolved by ordering the entities by the uuid as follows:
line 138 of uuid_commerce_product.features.inc inside function uuid_commerce_product_features_export_render
$code[] = ' $products["'.$uuid.'"] = ' . features_var_export($export) . ';';
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