Can I create an output bin file?

In the past I found the easiest way to do this was to use the USB Blaster and program all the required files into a real device on the real board.

Then we would either attach a USB PROM device reader/programmer to the device, and dump it's contents to a programming file.

Or in some instances the programming house wanted a physical device programmed with what we would want, so we would desolder and send one.

Not what you wanted to hear I suspect, but we needed to get it done and (then) Altera had no tools to build a flash device image from files.

AFAIK they still have no tool like that.