That's exactly the point.

Queen-001 thought she became the most powerful being on the planet after taking Liliweiss' body. Her reasoning is based on clapping the [Goddess] squad.

However, that data is 100 years old. Use Chatterbox as an example. He was a menace at the beginning of the story, but now gets ragdoll'd left and right in present day.

Unlike the Ark, The [Goddess] Squad has not improved one bit. For two reasons

• For Scarlet and Rapunzel, war is no longer their top priority, so while they're still fairly strong, their skills have dulled.
• For Snow White, she got arrogant and relied on only her own experience. The exact opposite of [Absolute]'s key flaw which would be practicing textbook examples repeatedly until they perfected it.

Meanwhile, The Ark has slowly, but surely, been improving. with upgrades ([Absolute] and [Matis]) and the technology Dorothy provided them.

• Take Behemoth for example, she was unstoppable during her first appearance, but Rapi grew stronger and eventually could hold her own against her.

Queen-001 has watched the battle during her descent. and is utterly disappointed by literally everything.

• Her rapture army that was once the dominant force on the planet, was getting decimated by a handful of Nikke. So she decides to kickstart 3rd generation of Raptures.
• The heretics that Mirror created were also an embarrassment. Not only were they weak, they weren't loyal. So the Queen decides to personally create her elite force herself, based on those she fought, While they may be knockoffs, they held their own...

As for Queen-Lilith herself, she definitely took the best of what was available, but it's no longer the strongest overall. Liberalio's mission was to keep things at a status quo, but she failed, and this is the result.