When multiple JavaScript modules are define()'d
using AMD and concatenated into a single file, are those modules still considered asynchronous?
Yes, they are still considered async.
While the module itself doesn't have to be loaded from disk, the modules do need to be executed and there is a call back made.
Because you can combine SOME modules into a single file doesn't mean you have to combine all -- nor does RequireJS assume all there.
It will run what it can from your preload and async load the rest.