If one had to guess, I would assume it would be the rate of decay. And I imagine that this would extend to other crafts, as well -- using Scrapper's tools would create items of low quality and quick decay, while Pioneer Craft items would be of superior / pristine / ultimate quality.
For the short time the tooltips were enabled, there were a lot of different quality items, so it only stands to reason that the tools used would determine the items quality. However, there's no current way for me to test this, so this is all just assumption and guess work.
Tribe mate of mine has a masters chisel for each quality...Master Foragers/Scrappers/Trappers/Pioneer Chisel but is unable to obtain any other master quality tools. Are they not it game or has someone else been able to learn another?