It looks like if you set your first samples "original" key value to C-1 you should be able to start from 1 or 2 in numbering the rest of your samples. (sometimes MIDI starts at 0).
In this day and age I wonder how many people build really in depth multisamples with the MPC? The work flow could probably be re-tooled, although I'm not sure autoloading is all that interesting.
One "workaround" would be to join all your samples into one file on the computer (or play them back and sample them as one file), load that one file and use NDC. I actually find this faster and easier, so maybe work ahead is a better word.

But I'm of the mindset that having a million one shot samples is a flow killer in general.