Well, this modification only replaces the main vbulletin logo div, nothing else is touched in anyway. No changes are made to the navbar template, apart from on the version for vB4.0.4 PL1 which has a slight CSS change for 'flush' fit the header to the navbar.
I noticed the mod you mentioned is for vB4.0.3, and that may cause issues. There were changes made to vB4.0.4 in respect to the header and headinclude templates.
As for adding a second navbar, it's not the sort of modification that would be beneficial to this current version. There are plenty of modifications for extending the default vbulletin navbar and navtabs, some free and a couple that are commercial. It is quite easy to code additional drop-down menu's, which in my opinion looks better on a forum than having multiple navbars.
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