If my character is making a charged item in the form of potions...
A Self range potion would only affect itself, I would think. There are applications for this, but not many.
I would say that an ingested potion simply doesn't work if it does not penetrate. It's still ingested. Further, the magus is promptly aware that, as the poisoned/tainted food is eaten, they have resisted a magical effect.
So non magical elixers are more effectively potent than magical ones?
R:Per effects in items only affect the item itself. As [strike]silveroak[/strike] TimOB pointed out, there are some applications of this for potions, but in general a potion should be R:Touch to (directly) affect the drinker with its magic.
Parma does not prevent you from drinking a potion. Remember, Parma protects you from being bitten by a CrAn fish, it does not protect the CrAn fish from being bitten by you. However, Parma prevents the potion from affecting you with its powers (unless it penetrates etc.) just as with any other magic item.
It's not clear what you mean when you say "non magical elixers are more effectively potent than magical ones". If you mean "a mundane poison is, all else being equal, potentially more dangerous to someone with magic resistance than an equally virulent poison whose powers are fueled by magic" the answer is yes, of course, because the latter can be magically resisted. Just like a "naturally" sharp mundane sword is more dangerous than one kept equally sharp by MuTe magic. Of course, through magic you can often achieve results that would be much harder, or just plain impossible, to replicate through mundane means.
Why should a charged item suddently become better, just because it takes the shape of a potion?
Its more a matter of the fact that it is activated by digestion which has certain implications...
That's controllable as a trigger action too. Ingestion might be enough, or touching the lips, whatever.
Personably, I'm fond of enchating the vial/chalice myself. Activation is "drinking from the vessel", so it still looks like a potion, but the liquid is not really as important.
Digestion is usually a rather slower process than ingestion. Not the same thing at all.