You can make a copy of the new tag file and put it in overrides/web/WEB-INF/tags/page.tag and this way it won't be overwritten but you run the risk of not getting a needed update file.
I'd rather get the updated file and have everything work smoothly, so I've been making a note of my 'customisations' so that I can redo them after I upgrade.
You'll fine the login file under web/modules/dglux/web
It looks like login.jsp is for the login.htm page (of course) and view.jsp is for the viewer page.
I have edited both files to include my tracking code. It works perfectly!
We are about to provide some customers with access to Mango and DGLux, so this will be a fantastic way to observe when and how they use Mango.
Nice idea, this is one of the features we want to add as we upgrade the Mango UI. For now I think you could add this into the /web/WEB-INF/tags/page.tag file. I've not tried that so if it doesn't work let us know. I don't think there is anyway to do that with DGLux.
I think that this will be a very useful feature (and quite easy to implement, I guess?). Note that some tracking (Google Analytics) require the snippet to be pasted before the </head> tag, and others (Piwik) require it before the </body> tag.
As an aside, I can really recommend Piwik to anyone who is looking for an alternative to Google Analytics. I use both, but Piwik offers a far superior level of detail and is easy to use, self-hosted, and free.