The Boys: V1 didn't just make Homelander immortal...
With the atrocious scaling of the final fight, though thematically appropriate, realistically should have Homelander fuck off at Mach 3 with no trouble, I believe the V1 gave Homelander to supercharge his powers for a short burst in exchange for debuffing him temporarily or even permanently.
The laser blast he let off at the end of episode 6 was orders of magnitude stronger than his usual beams, with the in-universe voughtintl post positing it to extend to the stratosphere and expand in width, and his subsequent laser beams lacked any kind of heat toward them.
He chokes out Soldier Boy with no difficulty but struggles to throw his teenage son who he ragdolled previously, break furniture or even make butcher bleed.
And lastly, he supercharged his speed and flight completely unnecessarily to throw knockoff Elon Musk into space, leaving him slower than Maeve doing her jumps in the first episode. Ironically, if he hadn't murdered Celon Tusk, he probably could have bounced pretty easily.
This is the most plausible explanation I can harebrain from the last 3 episodes, before Kripke hurls all over this in his next interview.