The whole film is Professor Bomba telling somebody the story.
This would account for the somewhat disjointed storytelling, seeing as Bomba himself is more than a bit scatterbrained.
Professor Bomba is slightly faster than ordinary humans.
When we see him from a non-Leafman perspective, he often seems to be moving and reacting and talking too fast. Also, this would explain how he discovered the Leafmen. If his speed differential is less than normal, he'd be a bit more able to see them naturally.
He has the axioms of Apokalypsi, that he used to build those helmets of his, and his obsession resulted in the creation of the leaf men.
The forest is still doomed.
We're told that the Queen Tara held the forces of decay at bay for the sake of balance. Now that the forces of decay have no heir, the balance is upset. Very likely all that new growth will suck up all the nutrients from the soil. Nutrients that would've been produced by the forces of decay. While not an immediate problem, it will eventually become an issue.