It is per document. Check this post for calculation and details How to read max_array_seckey_size setting (Version: 4.5.1-2844 Community Edition (build-2844))
One thing is remove members from index, So that query uses index and does Fetch (non covered index). If you have 100K elements that may not help, You can index on different field and array filtering can be applied post Fetch.
Also change the data model.
In 5.0 The limits are increased cc @deepkaran.salooja