Hey Brian,
Yes, I've seen your updated docs - many kudos to you for your efforts, sir - they are appreciated, by those of us less informed in the arcane ways!
The warning of 20+ years of modules waiting to be broke is probably the best reason to leave this sleeping dog.
As for your idea of how to upgrade prototypes - yes, something like this was what I had imagined. I had simply thought of numeric layers (1-999) for example, but I do like your idea of symbolic layers - that would allow different 'bins' for traits to be added and the order that each trait was added to the bin determined its order within the bin and the bins are pre-ordered.