Do potency runes deal magical damage? Nothing that I can see in the rules as written says that they do, except these two passages:
Some magic weapons and armor gain their enhancements
from potent eldritch runes etched into them. These runes
allow for in-depth customization of items.
Implies that runes magic items magical, but is not definitive.
Magical armor and weapons have the same Bulk and
general characteristics as the nonmagical version of the
same quality unless noted otherwise.
"Same characteristics unless otherwise noted."
The description of potency runes doesn't say that the weapon deals damage that is actually magical in nature (that is, bypassing nonmagical immunity):
A potency rune etched on a
weapon increases both the accuracy and the amount of
damage the weapon can deal.
And:
You can etch a weapon potency rune on a weapon
of the quality listed under the individual entry for the type of
rune. Runes of +2 weapon potency or stronger require the
weapon to already have the listed weaker rune, and etching the
new rune increases the existing potency rune to the new value.A weapon potency rune grants two offensive benefits. The
weapon’s wielder gains an item bonus to attack rolls with the
weapon equal to the potency value. For instance, an expert
dagger with a +2 weapon potency rune would grant a +2 item
bonus to attack rolls with the dagger.Second, on a successful attack roll, the weapon deals an
additional number of weapon damage dice equal to the potency
value. For example, a hit with the +2 dagger described above
would deal 3d4 damage instead of 1d4 damage.
Only that you gain a bonus to attack and that you roll more dice. There is no text that says that it is magical damage and no text that says that a rune applies its traits to the weapon its engraved on.
Compare to the Anarchic property rune:
A weapon with this rune deals 1d6 additional chaotic damage
against lawful targets
Fair point.
On the other hand, the Rulebook says on page 294 under "Immunity" that the creature with an immunity is immune to attacks with that specific trait.
Reading this, it is clear that a creature that has "nonmagical attacks" listed as an immunity is literally only immune to attacks with the "nonmagical" trait.
Therefore, if your PCs use any attack, even their empty fist, it will do normal damage unless that specific attack has the "nonmagical" trait.
I challenge you to find the "nonmagical" trait listed on any ability in the game. Maybe you can. If you do, then that is the attack that cannot hurt a shadow or other creatures with this immunity.
Or, to put it another way, we need to do two things here:
1. The devs need to write better definitions of their stuff. Omitting that runes make weapons magical is something of an oversight. Insisting that an immunity requires the attack to have that same trait makes some immunities worthless.
2. We need to exercise common sense and make these playtest rules work. Clearly, when you etch an eldritch* rune into a weapon, that makes it magical and its attacks should be considered magical. If not, then creature with immunity to "nonmagical attacks" are immune to all attacks except (maybe) spells. Or, alternatively, they are immune to all attacks with the "nonmagical" trait which is pretty much the same as being immune to nothing.
* "Eldritch" is defined as "weird or strange". Nothing magical about that. As far as the dictionary is concerned, my neighbor has a couple of really eldritch kids... However, it's commonly used in games and in the fantasy genre in general to mean "magical", which is what I assume the developers intended in this case.