Jhipster writes all your chosen settings in the .yo-rc.json file so you could generate it yourself with the desired parameters and then call JHipster - it will detect it and generate everything accordingly
There's probably a better way but this should work for Windows:
public static void main(String[] args) {
    String dir = "path/to/dir";
    String json = "{\n" +
            "  \"generator-jhipster\": {\n" +
                "<your settings>" +
            "  }\n" +
            "}";
    try {
        PrintWriter out = new PrintWriter(dir + ".yo-rc.json");
        out.println(json);
        out.close();
        ProcessBuilder builder = new ProcessBuilder("cmd.exe", "/c", "cd \"" + dir + "\" && jhipster");
        builder.redirectErrorStream(true);
        Process p = builder.start();
        BufferedReader r = new BufferedReader(new InputStreamReader(p.getInputStream()));
        String line;
        while (true) {
            line = r.readLine();
            if (line == null) { break; }
            System.out.println(line);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}