But save for maybe id or vbus monitoring (not pumping since we can't use it) there's no other use for twl3040 in our current use case. Basically, twl3040 should be out of the picture, and we'd need only accesses either SoC registers (via mapped i/o) or isp1707 registers (via ulpi, either using Nokia's musb_ulpi accesor functions or manually writing the SoC registers).
Also more importantly and along the lines of what you noticed is that you cannot get to the isp1707 while it is in standby (/lowpower protocol) or entirely shut down.