If the built in USB is using LUFA, IMO it's most likely emulated USB.
This means it'll be using much of that extra speed to talk to the PC, rather than running the machine. If you only intend to use the machine stand-alone (dump a file over USB, then disconnect) that would make sense. Otherwise a lot of your extra horsepower is just not going to get used for what you want.
Note: I've seen slower processors with on-chip USB (Leonardo-based design) trying to run movement on a Cartesian 2 axis bot, and the stuttering at the start of any action as they tried to do USB and even slow movement was not nice.
If you're making yourself a prototype, I'd look at making sure there is a serial port header exposed somewhere you can fall back on (using an external USB serial cable eg: FT232) if you intend to drive it a lot using USB.
This means it'll be using much of that extra speed to talk to the PC, rather than running the machine. If you only intend to use the machine stand-alone (dump a file over USB, then disconnect) that would make sense. Otherwise a lot of your extra horsepower is just not going to get used for what you want.
Note: I've seen slower processors with on-chip USB (Leonardo-based design) trying to run movement on a Cartesian 2 axis bot, and the stuttering at the start of any action as they tried to do USB and even slow movement was not nice.
If you're making yourself a prototype, I'd look at making sure there is a serial port header exposed somewhere you can fall back on (using an external USB serial cable eg: FT232) if you intend to drive it a lot using USB.