That section on negative numbers seems incomplete. It doesn't indicate how you write negative numbers instead talks about how normal binary computers use twos complement. Edit: I think I was assuming you'd only use 4 bit or 8 bit values with this notation.
As far as I can see the section on negative numbers was completely made up, or at least it is not sourced in the system's patent. The encoding was mostly defined as a way to transmit (and write down) binary data in nibbles (groups of 4 bits), it does not really concern itself with what that data encodes.
The one thing it does support which the wiki does not note, is a run-length encoding: if a syllable ends in R, then the segment until the next R is interpreted as a positive integer and a repetition count so HORBAR is 05 (5 repetitions of 0), and DIRHAHOR is 1516 (16 repetitions of a fully set nibble).
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