For 896 with 1 padding increase is zero and nothing should change. Nothing we did can change 896 to 989, which is a difference of 93. The most we add is 15 / scale. Maybe something is going on with scale. Remove your scale tags or remove / scale and see. Use alert so you can see the values, ie alert(increase);.

% is modulo. 40 % 16 gives 8 because you effectively subtract 16 until you have < 16, so: 40 - 16 - 16 = 8. 16 - (40 % 16) also gives 8. That means 40px would become 48px, which is correct (so far).

Later we do width * scale, which is the [scale:x] value. For that to work you probably want:

width += (16 - (width % 16)) / scale;
height += (16 - (height % 16)) / scale;

Dictated but not read.

Originally we did have numeric input for vertices, but found it simpler not to have it. It comes up from time to time, so we'll likely add it. The Spine UI needs to be adjusted to make space for it.

A stopgap could be snapping vertices to bones. Then at least you could place a bone numerically, snap vertex to it, and then delete the bone. It's not an ideal workflow because it takes so many actions, but it's more precise than the workarounds I mentioned above.

plunksville Sorry for the trouble. I would like to reproduce your problem, so if you don't mind, could you please send us the PSD file via email?: contact@esotericsoftware.com
Please briefly mention this forum thread URL in the email so that we know the context. I will check it as soon as possible after you send it to us.