Can you give me an example of exactly how you think such a thing would play out?
Sure. Say Varril is attempting a Combat check and plays Noxious Bomb (from S&S):
For your combat check, banish this card to use your Dexterity or Ranged skill + 2d6. You may additionally discard another card to add your Craft skill; ...
Varril chooses Dexterity and then discards another card to add his Craft skill to the check. He then discards (or recharges) another card to use his Divine skill instead of the Craft skill, so he is rolling a base of 1d10+3d6+2 on the check; which is strictly better than swapping out Divine for Dexterity and only getting 1d10+2d6+1d4+2 assuming no blessings are being played (as blessings would only add d6s instead of d10s).
Here's the relevant part of the Determine Which Skill You're Using (DWSYU for short)
Determine Which Skill You’re Using. Cards that require a check specify the skill or skills you can use to attempt the check. Each check to defeat or acquire a card lists one or more skills; you may choose any of the listed skills for your check. For example, if a check lists Dexterity, Disable, Strength, and Melee, you may use any one of those skills to attempt your check. Even if your character doesn’t have any of the skills listed for a check, you can still attempt the check, but your die is a d4.
DWSYU talks about checks, not skills, so you wouldn't be able to sub Craft. Same reason adding the Craft skill doesn't add the Craft trait.
That being said (highlighting the italicized), "listed skills" isn't limited to checks to defeat and checks to acquire; other checks also exist, like checks before you act.
Here's the relevant part of the Determine Which Skill You're Using (DWSYU for short)
Determine Which Skill You’re Using. Cards that require a check specify the skill or skills you can use to attempt the check. Each check to defeat or acquire a card lists one or more skills; you may choose any of the listed skills for your check. For example, if a check lists Dexterity, Disable, Strength, and Melee, you may use any one of those skills to attempt your check. Even if your character doesn’t have any of the skills listed for a check, you can still attempt the check, but your die is a d4.DWSYU talks about checks, not skills, so you wouldn't be able to sub Craft. Same reason adding the Craft skill doesn't add the Craft trait.
That being said (highlighting the italicized), "listed skills" isn't limited to checks to defeat and checks to acquire; other checks also exist, like checks before you act.
Varril's power as-written is not limited to the Determine Which Skill You're Using step. Vic's proposed wording clarifies what the listed skills for a check are, however Varril says any listed skill. To me, "any" does not mean "only the skill you're using for a check", it means "any skill," and Craft would qualify for that.
EDIT: re-reading the power, I notice that Varril also says "to use your Divine skill instead of any listed skill." which implies that it is, in fact, limited to the skill you used to determine the check. The "any" clashes with that though, and I don't think it's far-fetched for people to be really thrown off by that wording (any implies it's wide open, and the subtlety of "use" will be lost on many, including myself at first, and I like to think I have a good grasp of the rules). Varril could really stand some errata to evict that "any" and instead say "the listed skill" or some other word that doesn't make one misread the power.
