A friend and I had a discussion based on the Mystic Bolt faq, regarding whether it still gains a damage penalty from a strength penalty since we were told it mearely doesn't get strength bonus to damage.
Examples of the title are few and far between, but if it's true then Agile Maneuvers feat would still add the user's strength penalty.
I'm less interested in the faq, my friend and I both agree that it's not intended to gain a strength penalty to damage, and more the title as a general rule.
Intimidating Prowess (feat) is an example where the penalty is not replaced. I f you have STR 18 and CHA 6, your total bonus to intimidate is +2 (4 - 2 = 2).
It depends on how it's replaced. Sometimes it's not replaced, and you instead add both X and Y together, such as was mentioned in Intimidating Prowess example (in which case, it becomes language like "Add X in addition to Y for Z").
On to the replacement factor, we turn towards the UCRogue's Finesse Training:
In addition, starting at 3rd level, she can select any one type of weapon that can be used with Weapon Finesse (such as rapiers or daggers). Once this choice is made, it cannot be changed. Whenever she makes a successful melee attack with the selected weapon, she adds her Dexterity modifier instead of her Strength modifier to the damage roll. If any effect would prevent the rogue from adding her Strength modifier to the damage roll, she does not add her Dexterity modifier.
Bolded part says that it's a 1-for-1 exchange. There is a FAQ that says if you use, for example, an Elven Curved Blade, you would exchange 1.5x Strength for 1.5x Dexterity on Damage rolls as well (since people thought 1.5x Dexterity options were overpowered. Hilarious, truly). It simply alters the statistic, and goes on to say that effects which prevent (and by extension reduce) the Strength modifier to the damage roll, the same reduction (or negation) applies to the Dexterity modifier being used as well, reiterating that the Dexterity modifier is still treated in all other ways as a Strength modifier in terms of calculating damage.
However, then there's Steadfast Personality:
Add your Charisma modifier instead of your Wisdom bonus on Will saves against mind-affecting effects. If you have a Wisdom penalty, you must apply both your Wisdom penalty and your Charisma modifier.
In the UCRogue case, it specifies that you replace the attribute in question. Here, although it says it's a replacement (which it is), it then specifies that you must include any Wisdom penalties you possess to the associated rolls, whereas if it lacked that text, you wouldn't apply any sort of Wisdom bonus or penalty anywhere (because the feat makes those rolls key off of that statistic, according to a FAQ that states when, say, a Charisma skill becomes an Intelligence skill, that skill is considered an Intelligence Skill Check (for effects related to it).
In short, if you have a "Use X instead of Y for Z" effect, unless it specifies that you must use Y if it's Q or N (that is, positive or negative), as evidenced by Steadfast Personality, then Y has absolutely no relation to the equation that, thanks to whatever ability, results in "Use X for Z." Y is not a part of that equation result, meaning any positive or negative benefit Y was giving you is irrelevant and not factored into the solution.