I have no direct experience with USB audio on the keyboard, as my older PSR-E433 does not have this feature. However, I took a look at the online manual for the E363, and it does not list this function as being able to be saved to a registration. In the list of functions, it is grouped with things like the style volume and song volume that, on my E433, retain their values after the power is turned off. So, I would think that this function's value would also be retained when the power is turned off. But then again, just because the USB audio volume feature is grouped with the style and song volume (which do retain the settings upon power off on my E433), that doesn't necessarily mean that the USB audio feature has to retain the value upon power off, as well.
If you have a music store nearby that has the E363 on display, I would just go there and try it on the display model and see how it works. Turn on the keyboard, select the USB audio volume feature, change the value, turn the keyboard off, wait a minute or two, and then turn it back on and see if the value is remembered or of it goes back to the default of 100. If it goes back to the default, then that is just the design of the keyboard. The only thing I can think of to consider if you do this test is to determine if this feature is available and can be adjusted without anything being hooked up to the USB port. If not, then you'd need to bring your iPad and cable to the music store and see if they will let you hook it to their display keyboard for this experiment.
EDIT: I just thought of something. I doubt this is the case, but could it be possible that the iPad and/or the app is able to set the USB audio value on the keyboard? If so, then maybe the iPad/app is telling the keyboard to set it at the default every time you use it, but like I said, I think this is probably a long shot. But in a similar manner to above, try setting the level and turning the keyboard off and back on without the iPad hooked up and see if that makes a difference.