If you start with secondaries already on the mod, those secondaries bump up as you level it. If you start with no secondaries you wind up with the same number in the end, but since you are getting a new one each time instead of any of them bumping, you can't get them as high.
For example, a grey mod can't get more than 5 speed as a secondary. A mod that starts out gold with 5 speed can theoretically wind up with 29 speed.