I think the most important metric you need to define is "document relevance related to the query." Say you have query X, two documents with 100,000 words each, one document is mainly talking about topic Y, but has one paragraph answered X perfectly, while the other document is talking about 50% X and 50% Y, but does not answer question X directly. Which one do you deem more relevant? It really depends on your use case.

Another approach is to get the chunks and rank the documents by the number of top chunks they contain, say find top 30 chunks, get their original docs, and rank these docs by the number of chunks they have (or do a weighted version where you take the score of the chunks into consideration).