I've read the Vitkir section several times in Hedge Magic, and I'm a little puzzled by the description of Rune Magic when it comes to penetrating magic resistance.
On page 125 in the second paragraph of "Vitkar Magic," it says "The magic of the Runes causes a true and natural change to the target.... This also means that the target of the rune spell is not considered a magical thing, and does not trigger Magic Resistance. A target with Magic Resistance can still resist the effects."
Later on pg 137, under the "Ogre" rune, the first spell says "...if the effect penetrates their magic resistance...."
What the heck do these contradictions mean?
Does someone with Magic Resistance resist or not?!?!
It seems that one has to penetrate, just like the rules for Hermetic Magic.
But if so, then why all the confusing talk about "True and natural change?"
Finally, do Vitkir have any sort of magic resistance themselves?
Can they create wards?
As Tugsdual has noted, a distinction must be made between the spell itself, which affects a target, and the effect that the spell has on its target. Basically, affecting a target protected by MR still requires penetration, but a target affected by vitkir magic is not considered to be magical and thus bypasses MR by virtue of not being considered magical.
Example 1: Eirik decides to use Thurisaz/Mannaz to transform a hermetic magus into a goat. The script must successfully penetrate the magus MR in order to successfully render the transformation. If, however, Eirik decides to turn himself into a goat and headbutt the unfortunate magus there would be no need to penetrate as he is considered a "real" goat and thus is unresisted.
Example 2: Eirik wants to use Kauno/Othilda to set his sword aflame that it might deal greater damage to his enemies! The resulting flaming sword is considered perfectly natural and bypasses Magic Resistance as easily as any mundane blade. If, he had decided to try and set his enemy's weapon on fire (to hurt him), he'd have needed to penetrate so that the spell could have its effect (though the resulting flame would also be real and circumvent MR).
In answer to your other question, Vitkir don't actually exhibit any discreet Magic Defenses. Instead, it's expected that they will use their powers to create magic items that improve their ability to resist hostile magics by increasing Soak, Dexterity, Damage etc. Just about every rune has a General effect applicable to such usage.
To further your example: If the rune to turn someone into a goat was carved on the head of an arrow, and fired into an hermetic magus, I presume the arrow would wound the magus, but the Rune Effect would have to penetrate?
Maybe I misunderstand something. My understanding is that there are a few methods along these lines, but neither quite seems to fit. One option is to have the rune affect what it's on. That would mean you are trying to fire a goat from your bow. (This reminds me of cows in Monty Python's The Holy Grail.) The goat would then penetrate. But I don't think that's what you want. Another option is to carve the rune to affect a specific nearby (or via AC) target. If the spell penetrates the target becomes a goat. Do I misunderstand, or am I clearing things up?