Penetration applies to people/creatures, not spells.
callen did a big thread about the Aegis of the Hearth. I think he details it here, but I haven't read through the thread in a while
When it's discussed about the necessity for the Aegis to Penetrate, it means that for it to be effective in its ward functionality, it needs to penetrate. The wards and penetration issue is something that reared its head within 5th Edition shortly after being published. With respect to spells cast from outside and from within the Aegis, those mechanics are described within the text of the Aegis. The power of the Aegis is acting against the spell, or rather the spell must overcome the Aegis for it to be effective. Whether the Aegis actually penetrates the MR of a foreign magus, is, in my opinion immaterial. Magi can enter an Aegis that penetrates their MR, the warding capability only applies to creatures with might.