There is basically no difference between a standard tomcat and the bundle.
Data directory is a directory used by Liferay to store it's local lucene databases, the doc repository, etc. It does not have to be in the tomcat directory, it can be located anywhere and set in portal-ext.properties.
Deploy directory is the hot deploy directory Liferay checks for new plugins. When it finds one here, it will deploy it automagically while tweaking some of the files during deployment (modifies web.xml, adds dependent jars, etc.). This too does not need to be in the tomcat directory and can be set in portal-ext.properties.
License directory is probably related just to EE. I haven't checked, but this is probably settable in portal-ext.properties.
Logs directory is where the console logs will be written. This path is determined via the conf/logging.properties file and can be relocated.
The properties files are used by the ide and the liferay wizard, and readme is just that.
There are other differences between a stock tomcat and the bundle. You should use a comparison tool to identify all of the differences. For example, the bundle has a lib/ext directory w/ some additional jars and the directory is included in the conf/catalina.properties directory.
You can deploy Liferay to an existing tomcat, but it takes additional work on your part to do the deployment (see the doco for all that's involved).
The Liferay Tomcat Bundle is just an easy download package to springboard someone into using Liferay under Tomcat w/o jumping through all of the necessary hoops.
