Just to add my two mythic pennies:
It comes down to a discrepancy between a game balancing argument ("Allowing this would negate most MR at touch range.") and a rather logical thought ("In order to use an arcane connection I usually need to hold it. Stuff connected to the target in a more intimate way wields better arcane connections. Nothing is better connected to a target than the target itself.")
So, how to slove this without running roughshot over one of these two valid points?
In most cases where it is relevant I'd go with the "doesn't work" group and accept the in game argumentation that anything that has a MR is not in your hold mythtically speaking even if you touch it physically. So if somebody was sitting on Stellatus back and trying to PeVi him with touch spells he wouldn't get a penetration bonus from touching the whole dragon. If on the other hand he managed to rip off a scale or penetrated that thick scaly hide with his dagger he would remove that scale or the boiling blood from the creature's MR and could use them as arcane connections in order to boost his Penetration.
Unfortunately, this argumentation leads to two exceptions and one problem. The former two I am willing to accept, the later one still leaves me wondering:
First the exceptions:
a) A magus casting spells with a range bigger than 'Self' would get the bonus to penetrate his own MR because he is on the 'casting side' of the MR. This might come handy for junior magi in a dangerous situation where they don't want to lower their Parma, but it doesn't break the game, especially as this becomes a mote point some years later when they own talismans anyway.
b) If the target the magus touches doesn't have MR there is no barrier. This doesn't matter for penetration (as this isn't needed here anyway), but perhaps the caster wants to use a spell he has only learned at range: arcane or something like that. Well, let him.
Now the problem:
I can't use anything that has a MR of it's own as arcane connection to something it is part of (let's say a Diedne Quaesitor to his house for the Curse of Thoth). Here I am not really satisfied with the outcome of this thought.
ANd now to something slightly off topic, the validity of acorns and branches as arcane connections of different quality to the magical tree.
I am pretty sure both can work as arcane connetions, but I'd go with giving them different values, because essentially acorns are ment to be shed, and in my opinion would only qualify for weeks or months afterward. Most certainly the connection will be severed the very moment a new tree starts to spread from the acorn or when it is inside a boar's diggestive system.
A branch on the other hand is a much more integral part of the tree. Sure, it can com off, but so can a human's arm, but in both cases it's a severe wound. So a branch of sufficient size is rather comparable to a limb.
That's it from my side.
Alexios ex Miscellanea