Ok, so, I did some testing.
I maxed every pertinent skill for Rune and Hunting for Rune Weapon and wait for it...Marksmanship. I figured, ok, Rune Weapon has some sick bonuses, but Hunting as a LOT of piercing buffs. Can you make it work with a dex based Marksman build (obviously you can, and can it be comparable to Rune Weapon).
So, I put Int and Dex at 300 and used a couple of basic throwing knives with 10% piercing ratio. Clearly this can be buffed either way, but this is only for testing purposes.
I tested Rune Weapon tree maxed, Reckless Offence Maxed and Rune Word Explode and Burn Maxed against the Markeman Tree max with Art of the Hunt and Call of the Hunt.
Rune Weapon did more damage, and by upwards of 50%. Interestingly enough, if I attacked with Marksman right after maxed stacks of RW, then Marksman benefited a lot from the % damage increase. It seemed to do even more damage, but also, it appeared that, in general, RW outperformed Marksman on a single target. But that is where it got interesting.
I went to Sparta in the enemy camp where there are three targets side by side. I did two tests. I stood perpendicular to the middle target and started markmaning. Both side targets got hit with scattershot and both procced Runeword Explode EVERY time my main target did. It appears that the proc is checked once on the initial throw and then if you hit 9 fragments, then 9 runeword explodes. Wowzers. I then decided to test Punctureshot and lined up all three targets in a row. If I targeted the first target, passthrough seemed to go through it every time. I figured it would have been only 55% of the time, but it actually went through to the third target like 75% of the time. Not sure how that is all calculated. Even more so, if I targeted the last target, it seemed every attack went through.
If people want pics, I'll see if I can grab some, but when I attacked with RW, on the first target, some nice numbers went up and it went ding ding ding and sometimes the other targets would get hit with Runeword Explode. With marksmanship, my screen was full of yellow numbers. It was beautiful. Marksmanship absolutely rocks with Runeword explode. I'll have to test this with a real character in the game, but everything was lit up like a Christmas Tree. Also to note that it seems enemies can only be procced once. So, hit a target, and Explode procced, all three targets got hit with the initial dagger throw (2 if Reckless procced or 3 if Volley procced), then all three targets got hit with a scattershot (just 1) and all 3 got hit with a Runeword Explode (just 1). I couldn't tell if Runeword Burn procced on all 3 cause it is burn damage, but I am sure it did.
Some side notes. I didn't notice any projectile speed bonuses. And I couldn't test bleed either. Clearly the bleeding gets bonified from the other hunting skills and dex (nice additional damage).
Also, Thunderstrike loses a little bit of goodness as it doesn't get the Int scaling bonus to the lightning and electrical burn. Clearly Marksmanship doesn't have the other bonuses like leach health and energy, and it scales with Dex, not Int and you can't get a double dex like you can get a double int.
Marksmanship:
Rune Weapon: