Currently the only parameter for $extract is questionnaire-response. So, If I need some contextual information like resource ids I have to use the well known hidden field hack.
It will be more convenient to get this contextual information directly instead of passing it through hidden QuestionnaireResponseItemAnswers.

There is a launchContext extension that defines a contextual information required for questionnaire. launchContext used for the population process. It seems that all this contextual information is also useful during the form extraction process and may be a better replacement for hidden field hack

Solution
$extract should accept Parameters resource that containing all elements from launchContext and QuestionnaireResponse. All data should be passed to the extract engine.