Since JQL functions work as macros, whenever they return a big list JIRA needs to go through the whole list and validate the interim results before proceeding with the query.
Even though query is limited by other clauses, but JQL doesn't have smarts and calculates the context, even though a much more restricted context is provided by another clause.
Some improvements have been made to reduce the pain by batching and doing less work, but it doesn't scale beyond 100-200K issues.
We need to provide means to functions to override some of this behaviour.