I'm not sure why the timeouts are more generous in the browser vs. the projector, but I imagine it's primarily a product of the code path that gets hit. In the plug-in, the browser is handling the request on our behalf. In the projector, we're using our own network stack. I imagine that we chose a value that we thought was reasonable (and intuitively, 30 seconds seems like a long time).
There is no mechanism to configure the timeout in either ActionScript or the projector. You might want to consider breaking up the requests in order to stay under the timeout, especially if you're working under a deadline.
You're welcome to file an enhancement request to increase the timeout value for HTTP requests over at http://tracker.adobe.com/.