A list of the scans and my thoughts on them:
11x03: The Bad Seed
Grown Darkness: Amara-...-I am what you are becoming. And we are mightier than God.
Amara here states she is mightier than God.
11x09: Oh Brother Where Art Thou?
Sam: Is she equal to him in power?
Lucifer: Raw power? Sure. But she's got none of the experience. God is a master strategist. That's why you're here.
Sam: And why is that?
Lucifer: Oh, because God needs me to help put the cat back in the bag. [Laughing] He can't do it by himself. Seen that movie.
Lucifer states that in raw power Amara is equal to God and he was there when she was caged, so if he was wrong it wouldn't make much sense.
11x10: The Devil is in the Details
Sam:- ... -What if you're telling the truth? What if you can beat her?
Lucifer [yelling]: I can!
Sam: Even though the last time it took you, plus three other archangels. Oh yeah, and capital G, God.
God created and needed the 4 archangels in order to trap Amara. Makes sense, two beings of equal and opposite power cannot harm each other.
11x20: Don't Call Me Shurley [In God's Bar]:
METATRON: (Points at CHUCK.) You said... the safest place ever created. Created by you... to keep you safe from Amara! She can't touch you in here, can she?!
CHUCK: You're upset. I-I understand. And it's good to let it out. But, uh, let's focus on, uh, finishing my book.
If she was really stronger than God, she wouldn't have any problem breaking into the bar. But here, even though Chuck doesn't confirm it, he does not deny Metatron's observation that she can't touch him in there.
11x22:We Happy Few
CHUCK: We trap Amara. Put her back in the box.
DEAN: Wait, what?
CHUCK: Yeah. Well, you were right. She needs to be destroyed. But I won't kill her.-.....-
LUCIFER: Yeah, first time it took the combined strength of me and my brothers to weaken Amara before Daddy-O finished her off.
CHUCK: Even then it was close. Now with just the two of us, we'll lose.
Again it is confirmed that all 4 archangels and God were needed in order to seal her. Chuck says here that they will "lose", but I believe he means they will lose as in they will not succeed in capturing her, not killing her. Anyway, he outright refuses to kill her meaning he could if he wanted to, with the others' help).
CHUCK: Amara's looking for me. But I'm warded against her, for now. The second I drop the warding, she'll show.
If she was stronger in every aspect, why would a ward from a lesser being prevent her from seeing him. It can be argued that she not that nuanced in using her power, but Chuck doesn't appear to believe so.
AMARA: Hello, brother. (Panting) You cheated. Again. But ― '(With a yell, LUCIFER charges up behind her and spears her through. AMARA cries out. LUCIFER pulls the spear out, and she falls, but before he can stab her again CHUCK shouts.). CHUCK: Ah! Son.
Chuck prevents Lucifer from killing Amara here (cosmic balance and all that). However, it appears that she would indeed have died if she had been stabbed again.
11x23: Alpha and Omega
AMARA: That's your story. Not mine. The real reason you banished me, why I couldn't be allowed to exist you couldn't stand it. Yeah, we're equals. We weren't great or powerful because we stood only in relation to each other. You think you made the archangels to bring light? No. You made them to create lesser beings, to make you large. (She struggles to her feet.) To make you Lord. It was ego! You wanted to be big!
Amara now states that they are equals. [A sequence ensues where Amara 'overpowers' chuck but as I said in the OP, it has become clear that he did not resist her attack]
CHUCK: [Sighs] All right. Fine. 'The Darkness might—might have a weakness—'[Chuck walks over to Crowley and takes the bottle from his hand]
CHUCK: 'Light.''
CROWLEY: [sarcastically] 'He tells us now.'
CHUCK: 'What? I-I just wanted to trap her. 'I didn't want to murder her.'SAM: 'Okay, but now that we're trying to end her, how much light are we talking about?'CHUCK: 'I don't know. 10,000 suns set to supernova.
Chuck once again says he didn't want to kill her. He could have, in her weakened state. Also, if God himself in SPN is pure light, and Amara's weakness is Light, it makes all the more sense that he can indeed harm her, when she is weakened.
In summary, I believe it is justified to say that Amara is equal to God in their full power states.
