That depends on the skill. The synergy effects are differentiated according to whether learned skill or total talent should be more dominant. Thus some synergies depend on the raw skill level, others on the sum. When doing skill checks the total sum always will be considered.

Do you ever make Athletics, Find Weakness, Dodge checks? IIRC, Athletics checks used to be made periodically to exercise different stats, you could come up with situations where the other skills which are mainly-for synergy bonuses would be checked (you could hand out a "duck and weave" power where you get Dodge checks to evade missiles, but only while you are moving not while you are stabbing or casting spells?)

But if those skills aren't going to be checked ever they shouldn't have associated attributes, it's just going to confuse people.

I absolutely agree if you're not going to use the stat in calculation, it shouldn't have an associated stat - though this is simply another case where a manual would have helped solve the issue.

In fact, the game makes Athletics checks to improve stats. So +10 is clearly better than +1, even if you don't get any visible stat boosts. I had a troll character starting with Ap 2 having Ap 10 in no time when pumping Athletics to a high level.