My general take on this sort of scenario is first to eliminate all the redundant hostnames with round-robin DNS, through adding extra server power with software-based load-balancing in the interim with a solution like InterWorx, and breaking out database servers. If you do that, you should have a nice little server cluster that's crazy efficient.and scalable. You can add a CDN to the mix if you like as well. With all of that, SEO should work the same way as on a single server.
Sitemaps can then be generated dynamically really easily (in under 25 lines of code, most of the time).
If you just want a way to mirror static files, you'll want to look at rsync.
And finally, as for S3, my personal opinion is to stay away. I'm an SEO, but I also spent 7 years building a hosting company. Those solutions sound great in their marketing, but are scientifically less reliable than standard hosting, and you can verify that via public uptime tracking sites like HyperSpin.