Mammon Machine in the Black Omen

[Zaperking]

That wasn't really a projection if she took on her new form thanks to Lavos' power.

Yeah, it was a projection.  We know it is because after Crono & co. defeat her, she reappears in her human form before summoning Lavos.  I'll try to explain my take on how it worked - Zeal's powers on her own weren't enough, nor was the Mammon Machine.  So, she decided to amplify her powers through the Black Omen, and that's where you see her face and hands when Crono & co. fight her for the second time.  So it's not a merger in a sense like the Dragon Gods merging, but it is a merger in that she combines her powers with the Black Omen and it projects her face and hands.

I don't remember her reverting back. I thought she just died and then Magus is like "hmph" or something. And if it is a projection, then why was she hurt and bashed up. And Gaspar himself was happy for Zeal that she had died, so now she could rest in peace. It's kind of weird to think of Magus killing his own mother...

[DBoruta]

No, she definitely reverts back.  I believe this is the quote from her after the Crono & co. fight her the second time, right before she summons Lavos:

How dare you insects come after ME!

   Oh almighty Lavos, lend me your
   power!
   
   Mwa, ha, ha...
     
   At last, Lavos awakens!
   
   Compared with him, you are like
   germs.
   But, I...I shall obtain immortality!
   
   Indulge in such regrets in the next life!

Zeal was injured from that battle because she became one with the Black Omen - so when the projection of her face and hands were damaged, so was she.

[AuraTwilight]

Queen: Here, I can't produce power.... I've thought of something good. I'll put you bastards into the Demon Tool. I hope you're thankful.... To become a part of this ship! To become a part of me!! To become a part of Lavos-sama!!!

Oh. Ok then.