several interrelated questions here:
- it's been a while since i did the math, but iirc in general the dual-wielding full-attack bonus is a sufficient enough penalty that it brings the damage in line with a full-attack 2h weapon (which is the same as a primary attack w/ a 2h weapon), though there's still an advantage in that dual-wielding weapons have lower recovery time and you get two attempts to connect. so 2w is still arguably advantaged, just not as obviously as much as before.
- compared to a primary attack, a 2w full-attack is basically a 1/3 damage bonus (w/ rounding) over a primary attack - you have a -35% damage penalty on each attack, which means if you just somehow duplicated your #1 weapon you get a 65% attack and a 65% attack = 140% net damage. so, a sufficiently high primary attack damage bonus would make up for not getting a full attack, but no, a mule kick's damage bonus alone would not do it.
- keep in mind that the explicit damage bonus isn't everything. mule kick also gets an accuracy bonus. Accuracy also lets you do more damage over the long run, by increasing your crits, hits, and grazes compared to hits, grazes, and misses. i did some math a long time ago and in general (ignoring low/high extremes) each point of accuracy seemed to translate to ~2% net increase in damage (not the same as 2% damage bonus. for various reasons, a 3% damage bonus also translates into a ~2% net increase in damage, so in this way might and perception are very closely balanced in general). so adding on mule kick's +10 accuracy, its net damage bonus is closer to 36%, which is comparable to a vanilla 2w attack, but that math quickly gets complicated once you start adding in more bonuses and penalties. (complicated enough that when i say "back when i did the math" what i really mean is that i created a script that simulated the equations involved for thousands of scenarios to figure out what a general trend line was)
- similarly, penetrating strike has a bigger damage bonus in practice than on paper, because you should really be using it when you need the PEN bonus. in that vein, +2 PEN can constitute as much as a whopping +200% damage bonus when it helps you go from -3 PEN to -1 PEN. it's getting so, so complicated.
in the end i would argue though that just looking at damage is not the point to focus on for many abilities. Damage is just there to sweeten the cake a bit for spending a finite resource for knock down/mule kick. Ultimately the point of knock down/mule kick is a powerful interrupt (i almost don't even care that mule kick gets disorient, except as a way to get further +10 accuracy from helm of the white wind). Ultimately the point of penetrating strike is to help dps down a hard target in underpen situations, not just for the +25% paper damage + full attack.
sap can be better if all you care about is interrupt and resource efficiency, but it's not supposed to fill the same role as strike the bell, so you need to be clear about what each ability is actually trying to accomplish. if all you care about is damage on a rogue, for example, you really have no reason to do anything other than spam crippling strike over and over, even compared to sap. but the rogue has plenty of other abilities worth taking for reasons other than efficient damage.
(and it's worth highlightging that on potd, enemies end up with so much health in high-level fights that optimizing for damage on finite resource abilities is not a great idea imo anyway, so in that sense penetrating strike becomes kind of a trap choice)