Convenience and configurability
At work, I have access to many devices from DataPower to Cisco to F5, etc. Each of the config UIs seems to have a different layout, with some navigation on the side and others on top.
How do the usability rules change depending on whether something is the user's website something that needs to be configured?
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Either everything is fine and both work well - it depends on whether the method you choose is well implemented. For example: most routers have a menu on the left side and everyone uses these screens with minimal issues. Conversely, option dialogs always use tabs (at the top) and no one seems to have a problem there.
Even Microsoft will change their styles - the properties windows in Visual Studio and the options windows in MS Word 2007 have menus on the left.
This is a personal preference, although tabs work best with fewer options, and left navigation is better for more options. This is probably a rule of thumb, if anything.
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There is some evidence of better performance and user preference for left-hand menus than top menus. See http://www.usability.gov/pubs/040106news.html . I suspect its easier to scan a list of menu items to find interest than to scan.
If you have a hierarchical menu and cannot fit everything on the left, you can get comparable performance by combining the left menu with the top menu. The first user choice (top of the hierarchy) should be from the left menu, and the final choice (bottom of the hierarchy) should be from the top menu.
I see no reason why looking for a router setup to customize should be any different from finding a pair of socks to buy. Navigation is navigation, whether it's the user interface or the router's website. The differences you see are likely a result of different corporate traditions or aesthetic senses, not different usability principles.
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