We can send nested arrays in query parameters. If you flatten them, you can lost their structure and in most cases, make a huge mess with your data.
Actually, I will appreciate if you will explain bit more about your requirements

As I understand from the code, specifically from this expression:-

    ListVars = lists:map(fun
            ({K, V}) when is_binary(V) -> {K, binary_to_list(V)}; 
            ({K, V}) -> {K, V} 
        end, Variables),

only key-value pairs or elements of proplists are allowed in Variables List (I will say it fun constraint). So any nested arrays/List should be with their key. Since lists:flatten only works on deeplist it will not destroy any other list as if there is any list, it will obviously be inside a tuple (fun constraint). Example:-

%% This is what will happen (lists inside tuple are preserved) -->
lists:flatten([{k1,v1}, {k2, v2}, {k3, [v31, v32, v33, v34]} ]).
%% Output:- [{k1,v1},{k2,v2},{k3,[v31,v32,v33,v34]}]

%% Though this kind of list (nested array) will loose its flavor, but this is not gonna processed by our fun param constraint. It will be an error anyway. 
lists:flatten([{k1,v1}, {k2, v2}, {k3, [v31, v32, v33, v34]} , [discard1, discard2, discard3], {k4, v4} ]).
%% Output:- [{k1,v1}, {k2,v2}, {k3,[v31,v32,v33,v34]}, discard1,discard2,discard3, {k4,v4}]

My Requirement
Many times you might like to add another proplist in the url tag as in case, you need all the url parameters (which is already available as a list in _req.query_params). For that you might choose to operate on query params before, right in controller and make them suitable for url tag or in my case, just pass the proplist as it is, and url tag will automatically process it.

Please let me know if I am unclear somewhere or if I am missing something.