@Joejoe The use case you describe doesn't require you to alter the user's query. In fact adding metadata to a percolator query remained the same between 2.x and 5.x.
The main difference here is that a percolate time you use the percolate query in the search api. The percolate query doesn't contain the users query, but the document you like to percolate. If in addition you also like to filter percolator queries on previously attached metadata then you change the search request body that have a bool query with two or more must clauses. One clause for the percolate query and other must clauses for each metadata property you like to filter on. Similar how you would define filters in the 2.x percolate api.
Can you share rest / curl examples of steps you think you need to do? Then I get a better idea what you mean. I think we are somehow misunderstanding each other.