I head canon that the more liminal people become the more they notice Phantom and Danny are the same person. Ecto works as a natural camouflage for Danny (only his colors and outfit change so why hasn't anyone aside from Wes connected the dots ya know) so only his friends who where there at the time of his accident and Jazz are in the know at first. His parents are in protective gear 24/7 despite their terrible lab habits, so they don't see it.
The rest of the town gradually begins to see it and slowly change how they treat Danny and "Phantom". Nobody says anything, they just change how they behave. Slowly phasing out the bullying, extending due dates on assignments, redo's on tests, discounts when he eats out or extra appetizers on the house.
He is the towns secret hero so they will try to protect him since they already failed him once by letting him die. How else would he be able to turn into a ghost hero if not because he died at least once. He dies every time he does hero business and gets shot at by his parents so the town adults have become very protective.
When the Justice league shows up they give them the runaround because Phantom hid as soon as he registered who the visitors were. They leave after giving some autographs (the towns folks collected them for Danny/Phantom from the alien heroes because they know how much he likes space) but then the Bats come into town and the town is surprised when the Bats immediately identify Phantom as Danny. The natural ecto camouflage doesn't work on them since all of their deaths and/or contact with the pits made them liminal.
"We don't want to fight heroes-"
Batman correcting them mid speech. "Vigilantes."
"-but we will if you want to hurt Phantom." Adults armed with anything and everything from novels to pitchforks.
"This is all a misunderstanding, we came here to check in on him and offer a fellowship for young heroes." Red Robin who has a crush on Phantom for his determination and on Danny for his engineering and would definitely like to see more of him.
Dani brandishing a spear Pandora gave her just for these occasions "The red one wants to marry Phantom! get em!"
Danny blushing because he accidentally saw the face under the mask and Red Robin is very handsome. He would also like to get to hang out with other heroes is what he says when he intercepts the Dani incited mob trying to scare off the Bats
