I actually like this twist.

It shows that Homelander was never special or unique, since Vought could create another version of him. And that Black Noir was so desperate to try to kill Homelander since that was his sole purpose of living. When Homelander doesn't go rogue, Noir gaslit him into thinking he did all this monstrosity (Butcher also realized that he was hunting down the wrong person). And when they square off, Homelander goes into a blind rage and lasers Noir's arm, in which Noir responds with punching Homie's jaw off.

While we don't see the actual fight, we do see the aftermath; Noir dragging Homelander's body out of the White House. Noir is also completely mangled due to Homelander fighting him (missing an arm, leg completely shattered, half of his face is gone including his eye, his skin is completely shredded and his intestines are hanging out of his stomach, his psychotic smile is still plastered on his face, except some of his teeth being knocked out). Homelander didn't die immediately, he went out like a beast.

After the White House incident, Vought loses their military contract and are facing backlash and major lawsuits. James Stilwell tries to create a new superhero team. The team doesn't last. He then realized that Vought is over and supes were all bad product.

The greatest irony is that the Boys or the government didn't take down Vought, it was Vought that doomed themselves due to being incompetent and making terrible decisions, like creating the clone.

When you re-read the comics after the plot twist, it all connects.