Ooops, I was thinking of tomcat:deploy/redeploy etc., going to a standalone Tomcat; not tomcat:run which is indeed for embedded. So you're asking for the simpleWebapp example to be converted to running on a single Tomcat (embedded or not). I think that's still a non-starter, as the sample webapps are trying to mimic a production environment, the key relationships (the last two columns in the README I provided) would be lost (nothing would be learned) and the Tomcat configuration (such as installing the RP plugin) either much harder to do embedded or no longer available due to embedded usage. We'd be making you happy only up to the point when it's time to learn about the key relationships while increasing the difficulty to learn the latter from everyone else. So I don't see your recommended change being an improvement, but perhaps other team members think otherwise.
You don't need embedded Tomcat to debug in Eclipse (http://www.jroller.com/gmazza/entry/eclipse_debug_web_services), and the IDE would probably work even if you're debugging two Tomcats simultaneously (have Eclipse listen on different ports). It's probably clearer to debug that way, and further, you can see the full key validation occurring if you use multiple Tomcats. At any rate, the sample can probably already be loaded on one Tomcat, it's just that you will need to follow the configuration instructions but load to one Tomcat instead of two. I still think it's preferable for you to go through this extra work so the multiple Tomcat learners (who already have a tough job) have it easier OOTB than vice-versa.