Hi there!
The point here is that the app in question either validates the XML according to the DTD or it does not. Or, put in another way, either it needs to, or it needs not.
As long as your app is not required to validate the doc, you don't need access to the DTD, the DOCTYPE tag is just ignored.
You should use DTD validation if you expect your app to receive input from external users, whose XML you will not be able to verify before input.
You can not turn off validation in an XML doc. I don't know what 'weblogic' is, but probably (considered today's connectivity conditions around) it will not go to the web to check the DTD for a configuration file (if that's what 'web.xml' is).
The point is that as long as you, as system administrator, are able to keep the config files proper, it would be a serious flaw in any system to let you have downtime because it cannot access a public DTD.
This may change in the future, when connectivity is more or less assured everywhere.
Good luck with your project!
Regards,
Marius