The firmware is what controls the hardware and its settings. So the hardware needs to know what kind of throttle linkage is attached. And the settings on the handheld are enabled by the firmware on the hardware. The EFI software runs on your computer and can be used to change settings, but only if the firmware supports it. From what I read on the Holley Sniper forum, the firmware must be upgraded to a version that supports progressive linkage. And the EFI software has not been updated to directly support the progressive linkage yet. Unless it has recently been updated, that is. So you can do some data logging and tuning with the software, but the actual settings for the progressive linkage are only in the handheld. Future EFI software will eventually have more support.
I would think that if you added a progressive linkage without the right firmware and settings in the handheld you would have big problems the first time you attempt to start the engine. In theory, the settings in the handheld should be enough to run the engine well without needing a computer. That's what they tell us anyway.