Is getting AP runes good for waveclear?( Instead of magic pen )

yes ap runes are better for waveclear pen hardly effects minions. BUT 9/10 times you want magic pen just learn to farm better

Techinically yes, but its gonna gimp your mid game. And if you fall behind you wont do shit until you complete void staff at like 50 minutes.

Minions don't have resistances unless promoted, is a super minion, or is under the effects of baron or super minion auras.

depends on champion since the actual dmg you get from ap depends the ap ratio of the abilities. Also, flat magic penetration is still good if they don't have MR because that mpen will count towards a negative value which amplifies your magic dmg.

I think they removed MR from minions completely. So the short answer to your question would be yes, if you're using your abilities a lot to waveclear early on (usually gated by mana though).

THAT SAID: AP marks are really inefficient (like half the value of AP glyphs). Wouldn't recommend.

But if you're talking about Quints then AP is almost universally a better option than mpen.

I find Pen Marks and AP Quints are the best, and if I have an AD matchup I will actually run CDR on my Glyphs.

It's not so much about waveclear as it is about AP scaling, and the damage difference (particularly at low levels) with the champion you are referring to. You can look up the MR and Armor values of minions, the damage scaling that MR/Armor Pen bring, and the Scaling ratios for your champ to see what gives you the most damage

ORRRRR

Just test it in game and see what works better for you! Personally, an amplifying tome, or dorans ring can help a lot at the start for last hitting easier, but that depends on the champs I play.