Ah.
The location of the webapp doesn't matter. Tomcat will treat any deployed webapp the same way as any other deployed webapp. However, the directives in web.xml apply to the webapp as a single application (which technically, it is).
So to provide alternative error pages, you'll have to do some work.
1. You can have the exception be caught by a
JSP, instead of an HTML page and put logic in the JSP to redirect to the desired error page.
2. You can have the servlets trap the error and redirect to the error page directly. Which I recommend, because it offers the ability to better report and clean up on failues. Doubly so if the majority of errors go to standard pages, and you only want selected servlets to use per-servlet pages. Variation: subclass the HttpServlet base class, add the desired error handling, then use that class as the base class for your servlets.
3. You can code a ServletFilter and have it trap and redirect responses going out with a "500" Response Code.
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.