Hey Mark -
Short of doing something fairly unnatural and unsupported/undocumented (like hacking the HTML partials of the web portal or CSS files), there really isn't a way to do this.
Can you explain what you mean when you say that a dashboard gets left aligned when you embed it? Maybe a screenshot with what you "see vs. what you want"? Embedding really is the right solution based on your requirements. It almost sounds like you just need to modify the "hosting page" to center-align the div or iframe you're working with. This would have less to do with Tableau, and more to do with web dev.
Also, there is a open case related to being able to collapse the top nav bar which was an option within 9.x, but is yet to be built-in to 10.x