How Eclipse IDE deploys webapps is its internal implementation detail, and in my opinion, irrelevant.
I don't know what "malformed" URL you are referring to, but there is absolutely no difference in a web app URL whether it's Run on server from Eclipse, or deployed manually in a tomcat installation.
If you are expecting
http://localhost:8080/JSPServletTutorials/WEB-INF/web.xml to work, then your understanding of JavaEE web applications is faulty.