Good idea. Unarmed fighting is currently totally out of the question for most classes.

I think it would make more sense to directly buff shadow touch. A buff that made unarmed combat viable in general would either massively buff monks and beastfighters, or muscle in on their niche as unarmed specialists. Any buff of a lesser magnitude is just a roundabout way of buffing shadow touch, since other classes still won't use unarmed combat.

As for your specific suggestions:
1) If the damage boost is good enough, this will be a huge buff for monks and beastfighters. If the damage boost isn't, this is just a small buff to monks, beastfighers, and shadow touch.
2) Same considerations as 1)
3) Those boosts are not enough to make general unarmed combat viable. This amounts to making a small buff to shadow touch, for necromancers who use it a lot.

I would suggest giving shadow touch a chance (25% maybe) of bypassing PV. This is probably enough to make the ability usable against some tougher enemies, and can be explained as the necromancer making their hand temporarily incorporeal.

I agree that Unarmed would likely be unused for the majority of classes, but I would guess that most monks forgo unarmed combat in lieu of using weapons as there are no penalties. Setting each set of knuckles at the proper danger level would help keeps H2H more viable in the late game - and eternium vs iron dagger provides an extra damage dice an +7 damage, while a 2HS provides 3 extra damage dice and +15 damage when comparing iron vs eternium. So if brass knuckles provide +3 damage, I would imagine each additional type of knuckle to provide an additional +1 damage, with the eternium maybe providing +8-12 with a reasonable cap of +12-13 with scrolls - not a massive improvement over the +3 from brass knuckles and on par with higher tier weapons found in the late game.

I've never played a beastfighter so can't comment on their damage scaling, but I've played a few monks and have always ended up using weapons as H2H is less viable - even the instakill ability the Monk gets carries over to weapons (the wiki incorrectly states it as being H2H only). Also, keep in mind that you are also using this item in the gloves slot instead of elemental gauntlets, archery gloves, dragon hide gloves, etc. Also it might be nice to smack back ratling duelists and swordsman if you can't reach your weapon.

If the direction would be to boost shadow touch giving 25% Penetration might be a bit OP (sources of penetration should be rare), so maybe +Crit would be better. Just my opinion though.

Wonder if it would be too unbalancing for knuckles/boxing gloves to receive the same random extensions that weapons do...

I suggest making knuckles (brass or other) work like heavy/iron boots for kicking. (boots PV is added as bonus to damage).

PV improvement limits total gain and it uses mechanic already present in the game.

I think prefixes/suffixes on knuckles would be too much.

I wasn't aware that boots' PV adds bonus damage - I assumed it didn't as spiked boots add bonus to kicking damage. That's actually a great idea and would still make attaining high numbers quite difficult with a cap of +8 or so, unless you go nuts with smithing scrolls of protection.

I support the ideas stated. Although H2H still would be less attractive than range combat and mage it might be at least sometimes viable alternative to weapons.

Don't forget duelists in your consideration of H2H. Apparently their class powers make them pretty effective at H2H (could be a bug).

I support everything but number 3:
If any change is supposed to be made to unarmed damage from the skill, it should go directly towards the skill bonus - it is completely illogical for there to be an increase in the variable part that would benefit ONLY those classes that are supposed to be bad at unarmed melee. If anything, monks and beastfighters should benefit MORE from the unarmed skill, instead of less!

But the one thing that I'd like revisited is the differences between "unarmed" with shield vs true-both-hands-empty unarmed fighting styles - if anything should really be changed/affected, it is this.