Kitz suppressing the evidence is due to direct alien involvement.
"Yep, Humanity isn't ready yet" was their report. As a result they notified certain government officials to suppress the evidence for x amount of time, until Humanity is ready for another evaluation. God created the Portal Network.
Ellie and Matthew are BOTH right. The Firstborn (the aliens of 2001) created the Portal Network.
Long before they Ascend to a Higher Plane of Existence. The Vegans are hideously ugly.
Another reason why one of them appear as her dad since they don't want to scare her. The shimmering dots represent known habitable star systems.
Earth is one of them, and the rest are others that also made contact with the Vegans. The Vegan who took the form of Ellie's dad did say that a few chose to respond. The religious fanatic Joseph is misogynist.
He comes from an old school teaching where women are sinful and seductive (e.g. Samson's lover Delilah). His Death Glare towards Elle is because of his fear that a woman will bring the end of the world from alien contact ("witch summoning demons"). First Contact created a new religion.
The chorus singing "Hail to Vega" in the style of "Hallelujah" is part of a group that believes Jesus was an alien sent to Earth to help humanity.