We can set the default character encoding to use for reading request bodies by ServletContext#setRequestCharacterEncoding (since Servlet 4.0).
I think that the character encoding for HttpServletRequest#getReader can be set using ServletContext#setRequestCharacterEncoding(*).
But the reader that HttpServletRequest#getReader returns seems to decode characters not using the encoding set by ServletContext#setRequestCharacterEncoding.
My questions are:
- Why 
ServletContext#setRequestCharacterEncodingdoes not have an effect onHttpServletRequest#getReader(but it have an effect onHttpServletRequest#getParameter)? - Is there any specification describing such 
ServletContext#setRequestCharacterEncodingandHttpServletRequest#getReaderbehaviors? 
(I read Servlet Specification Version 4.0, but I can't find any spec about such behaviors.)
I have created a simple war application and tested ServletContext#setRequestCharacterEncoding.
[Env]
- Tomcat9.0.19 (I don't change any default configuration)
 - JDK11
 - Windows8.1
 
[index.html]
<!DOCTYPE html>
<html>
<head>
    <meta charset="UTF-8">
</head>
<body>
    <form action="/SimpleWarApp/app/simple" method="post">
        <!-- The value is Japanese character '\u3042' -->
        <input type="text" name="hello" value="あ"/>
        <input type="submit" value="submit!"/>
    </form>
    <button type="button" id="the_button">post</button>
    <script>
        document.getElementById('the_button').addEventListener('click', function() {
            var xhttp = new XMLHttpRequest();
            xhttp.open('POST', '/SimpleWarApp/app/simple');
            xhttp.setRequestHeader('Content-Type', 'text/plain');
            <!-- The body content is Japanese character '\u3042' -->
            xhttp.send('あ');
        });
    </script>
</body>
</html>
[InitServletContextListener.java]
@WebListener
public class InitServletContextListener implements ServletContextListener {
    @Override
    public void contextInitialized(ServletContextEvent sce) {
        sce.getServletContext().setRequestCharacterEncoding("UTF-8");
    }
}
[SimpleServlet.java]
@WebServlet("/app/simple")
@SuppressWarnings("serial")
public class SimpleServlet extends HttpServlet {
    @Override
    protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
        // req.setCharacterEncoding("UTF-8");
        System.out.println("requestCharacterEncoding : " + req.getServletContext().getRequestCharacterEncoding());
        System.out.println("req.getCharacterEncoding() : " + req.getCharacterEncoding());
        String hello = req.getParameter("hello");
        if (hello != null) {
            System.out.println("hello : " + req.getParameter("hello"));
        } else {
            System.out.println("body : " + req.getReader().readLine());
        }
    }
}
I don't have any servlet filters. The above three are all the components of this war application. (GitHub)
Case 1: When I submit the form with a parameter 'hello', the value of 'hello' is successfully decoded as follows.
requestCharacterEncoding : UTF-8
req.getCharacterEncoding() : UTF-8
hello : あ
Case 2:
When I click 'post' and send text content, the request body cannot be successfully decoded as follows.
(Although I confirm that the request body is encoded by UTF-8 like this: E3 81 82)
requestCharacterEncoding : UTF-8
req.getCharacterEncoding() : UTF-8
body : ???
Case 3:
When I also set the encoding using HttpServletRequest#setCharacterEncoding at the first line of the servlet's 'doPost' method instead, the request body successfully decoded.
requestCharacterEncoding : UTF-8
req.getCharacterEncoding() : UTF-8
body : あ
Case 4:
When I use http.setRequestHeader('Content-Type', 'text/plain; charset=UTF-8'); javascript, the request body successfully decoded.
requestCharacterEncoding : UTF-8
req.getCharacterEncoding() : UTF-8
body : あ
Case 5:
When I do not call req.getParameter("hello"), the request body cannot be successfully decoded.
requestCharacterEncoding : UTF-8
req.getCharacterEncoding() : UTF-8
body : ???
Case 6:
When I do not call ServletContext#setRequestCharacterEncoding at InitServletContextListener.java, no character encoding is set.
requestCharacterEncoding : null
req.getCharacterEncoding() : null
body : ???
[NOTE]
(*)I think so because:
- (1) The java doc of 
HttpServletRequest#getReadersays"The reader translates the character data according to the character encoding used on the body".
 - (2) The java doc of 
HttpServletRequest#getCharacterEncodingsays"Returns the name of the character encoding used in the body of this request".
 - (3) The java doc of 
HttpServletRequest#getCharacterEncodingalso says"The following methods for specifying the request character encoding are consulted, in decreasing order of priority: per request, per web app (using ServletContext.setRequestCharacterEncoding, deployment descriptor)".
 
- (1) The java doc of 
 ServletContext#setResponseCharacterEncodingworks fine. When I useServletContext#setResponseCharacterEncoding, The writer thatHttpServletResponse#getWriterreturns encodes the response body by the character encoding set by it.