ok, so the plugin is multisite aware in the sense that it uses blogs.dir/2/files etc. I didn't realize that. However, the configuration settings need to be setup independently for each site. While I can see some people may like that flexibility, ideally it would also have the ability to be setup once for all network sites. Obviously, using the admin form fields to setup hundreds of sites manually is impractical.
I wasn't hired specifically for this job, no, but I am an employee. I chose to use WordPress even though I'm not familiar with it, since the code base seems relatively small, simple and clean. I am familiar with cloud services and AWS (though mainly from the Java world, I have written several PHP apps that use S3/CloudFront/SimpleDB).
So, I could modify the plugin to automate all the necessary pieces, but I honestly don't want to generate 312 S3 buckets and 312 CloudFront distributions when one would do perfectly fine.
Yes, I could always fork the code - but this is why Linux has never gained wide acceptance in the general public - because it is a bunch of pieces being developed by people serving their own interests, typically without serving the greater community (i.e. the public). Even when some organization stands-up and tries to take on that role for those who want it, the rest of the self-interested project communities shout them down (cf Ubuntu).
So, no, I won't fork CDN Sync Tool if I can avoid it. What I may do, is look more closely at the code for both CDN Sync Tool and any other similar plugins and decide which is easiest to adapt to my requirements, then contribute any code I write back.
Thanks for the pointer.