Perhaps surprisingly, those are the only two deviations from what my troupe and I had always believed were the rules as intended.
As for Supernatural effects that have neither casting totals nor Penetration, we read on HMRE p.7, and I think this is fairly uncontroversial:
If a hedge wizard casts an effect towards an Aegis, the effect must Penetrate the Aegis to be successful. This includes transportation effects; for example, a folk witch cannot fly through an Aegis unless her Penetration Total exceeds the level of the Aegis."
Now, a supernatural effect without Penetration, as far as I understand it, does not penetrate even MR 0. If the rules are intended to be different, then probably a clarification should be extended to the section on Magic Resistance, since in ArM5 (p.85, the last paragraph on Magic Resistance) we read:
If the target of a spell has Magic Resistance of 0, she is only affected if the penetration total is 1 or greater. Thus, Magic Resistance 0 is substantially better than no magic resistance.
If there is no penetration total, there is no penetration total 1 or greater, and thus the effect does not penetrate. And thus the effect fizzles out in an Aegis of any Level. For example, a lesser purifying touch should not be able to penetrate MR by the rules as written and as intended, fizzling out in an Aegis of any Level.
As for Nightwalkers: I think they were never intended to be an exception to the "standard" rules, though the author might have misread those rules (or failed to read the general text for Hedge Wizards on HMRE p.7). There is no mention of straying in relationship with the Aegis or MR anywhere in the mechanics section of the Nightwalkers chapter, strongly suggesting that the author did not intend to change anything. It's only in Saga seeds that we read (HMRE p.118):
Nightwalkers have no Might, so they are not held at bay by the Aegis of the Hearth
Now, this is technically true. A Nightwalker is not held at bay by the Aegis of the Hearth, and can simply walk into one. But as I read it, a straying Nightwalker is blocked by Magic Resistance, and the straying effect fizzles out upon entering the Aegis. I cannot find any text in the Nightwalker section that is technically incorrect if Nightwalker powers cannot penetrate MR or the Aegis.