I see that a USB mouse driver is included, is this in a rom to enable use of the mouse during early startup?
No. You can't include ROM on any clockport to be read during the autoconfiguration process (which doesn't know anything about clockports). In contrast with the ALGOR or HIGHWAY + ROMulus, you can start Poseidon right before anything else in the machine (as Autoconfig explicitly uses ROM for this purposes). But in any case: early startup works only with BoingBag2, as the previous versions of the ROM code did touch directly the CIA ports for checking mouse buttons.
If your Amiga has been started once, and the ROM updates have been installed (and Poseidon has been made resident) you can use your USB mouse for the early startup stuff.
Sorry for that, but it is a quirk in the hardware layout of the Amiga one has to live with.
Michael