Well, I think I looked at other ships for an example as to how to do it and saw that it depended on what is being done to the ship and that is what I did with my ships. It depended on which refit/reconstruction level was being applied to the ship
Using one quick French example from Q4/1943...
Idle Dockside: - Tanker Seine converting to naval auxiliary. 1451 tons required. 1451 tons added in Q4/1943. Conversion completed.
Now her light displacement is 9673 tons. 1451/9673 *100 = 15%
15% =/= 25%
So if you are adding a radar and add a buch of 20mm and 40mm guns to the design, it will be a 5% job. If you are going to add some automatic 3" guns to the design and put some light armor plating on the outside of the ship for some protection, then it will be a 25% job. Also if the ship is less than 3000 tons light, then the <3000 tons percentages are valid.
At least that is how I understand it how it should be done by looking at other examples.