I actually don't like how this works, currently.....
First of all, way more weapons don't do stun dmg natively anymore (which I'm ok with in a way, a baseball bat is actually a pretty deadly weapon, but even a "sap" does Physical dmg now?!? C'mon)
Secondly, if you're trying to knock someone out without killing them, it doesn't seem to me like "splitting the difference" actually helps with that. Assuming stun and phsyical tracks are of similar size (usual) you just wind up knocking them out about the same time you they start dying, but it takes twice as long.
The most reliable way to do stun dmg is just to keep the dmg value below the armor.....unless with split the dmg does it count the whole dmg, or just half for beating armor? If it's just half, then an lot of the time you WILL wind up doing all stun dmg. That's a decent rules questions, actually.