FYI I’ve documented this at https://www.xwiki.org/xwiki/bin/view/Documentation/AdminGuide/Installation/InstallationWAR/InstallationTomcat/#HThreadLocalErrors
Note that I was wrong above. These SEVERE ThreadLocal errors happen independently of how you stop Tomcat. What’s important is that the JVM is stopped when restarting XWiki. If you do that then you can disregard these warnings.
In any case these should’t impact the shutdown speed of XWiki I think.