I missed this before, but you are correct, thistleknot. These settings are in File->Options->Roles.
I set the values to: Attributes 0.15, Skills 1.0, Traits 0.05 and Role preferences to 0.05 and sorting by skills is now saner, but still incorrect.
My assertion that this method of doing it is bogus still stands, however. Things like Starts, Skills and Traits are fundamentally different and you
cannot make a weighted arithmetic average out of them, same as you can't make a weighted arithmetic average of temperature and mass and claim it means something.
Even if you could, there is no way to do it without knowing the formulas or at least substantial research into how skills influence stats. All I ever found was that high stats increase the speed of a job (but by how much is unknown) and of course that agility, strength and carry weight influence walking speed (there are formulas for this somewhere). There is some scattered data on things like "creativity makes engravings more varied" and some old research suggesting that material and item preferences influence quality of the item by a small margin, but beyond that I found nothing.
My conclusion so far is that (at least in my mod's case) skill level and skill rate are everything and stats barely even matter, except for soldiers and for walking speed.
the way Splinterz Dwarf Therapist is setup is to sort things based on the calculated role %.
I've noticed and am very unhappy about it. I'm trying to convince splinterz to fix it. How come no one noticed this bug before?
There is an option inside that allows you to sort by skill exp (i.e. the old way of doing it).
I haven't found it, but setting everything except skill to low weights alleviated the problem.