Weird question. Made a character with the trait Wisdom in the Flesh.
"Select a Str, Con or Dex-based skill. You may make checks with that skill using Wis instead, and it is always a class skill."
In the case, went with Disable Device (making a terrible character concept Samsaran Oracle focusing on Ancestry to make essentially a weird fighter/rogue/healer hybrid). Making it a Wisdom-based skill though, would it still apply an Armor Check Penalty. It doesn't say so under the trait, so my assumption is probably no, but I'm not sure. And avoiding my -3 (Armor Expert is my other trait reducing penalties by 1 on my medium armor) on what it looks like may be my character's job in Skull and Shackles may be helpful.
I say no, though I have seen it disputed.
Alternate Ability Score-Based Checks: If I change the key ability score of a skill (or other check), for example, if I change Knowledge from Intelligence to Charisma, is it no-longer an Intelligence-based check? Is it now a Charisma-based check?
Generally yes—at the time of rolling a check, if you substitute the ability score, the check is now based on the new ability score. In the example, at the time of rolling, Knowledge would now be a Charisma-based skill and not an Intelligence-based skill for you, which would affect things like feats, spells, or items that grant bonuses on checks based on their key ability score (like circlet of persuasion). However, if you are adding a second ability modifier to a check, this is not the case. For instance, when adding both Wisdom and Dexterity on initiative checks, initiative is still a Dexterity check, not a Wisdom check. Also, this changes the check only at the time of rolling, so this does not change static class features or options made during character building such as your class’s class skills. Classes that receive “all Intelligence-based skills” as class skills, for instance, are the victim of sloppy writing, and furthermore sometimes effects might muddy the water by only changing the ability dependency sometimes and not others, which is why you check the new dependency only for a specific given roll.
So, at the time of rolling you will always find that Disable Device is a Wis-based check, not a Dex-based check, and therefore ACP does not apply.
However. Paizo helpfully put "Armor Check Penalty" in the skill description of each skill that (normally) has it, even though this is redundant with the general rule. I have seen it argued that that should be read as solid rules, not just a helpful reminder, which means that since Wisdom in the Flesh doesn't specifically make it vanish, it doesn't vanish, and ACP still applies. So you should check whether your GM is willing to disregard that argument.
However. Paizo helpfully put "Armor Check Penalty" in the skill description of each skill that (normally) has it, even though this is redundant with the general rule. I have seen it argued that that should be read as solid rules, not just a helpful reminder, which means that since Wisdom in the Flesh doesn't specifically make it vanish, it doesn't vanish, and ACP still applies. So you should check whether your GM is willing to disregard that argument.
I will. Thank you for the full bit on it (and not just calling out my bad build :P). I'm our table's rules guy though, and this will be his first game running (we cycle GMs), so I'll present it to him as both are technically viable. Since ACP does specify Str and Dex-based skills.