You are getting confused by the two different levels:
1) Your soldier is always your level. All combat involving your soldier takes place using the adjustments based on the difference between your level and your opponent's level.
2) All Skirmish trait upgrades have a level associated with them. The cost to buy an upgrade is base cost 100% when the upgrade is the same level as your character. You want the lowest cost to purchase a Skirmish trait upgrade. Do not buy any upgrades until after you level cap.
In summary, buying an upgrade under your level you get a discount. Same level full price. Higher level you pay extra. The more the difference in levels the bigger the discount or penalty.
Unless stated otherwise, all content in this post is My Personal Opinion.