I would say I am more interested in exploring the teens interpersonal conflict of faith incited by the arrival of aliens rather than exploring humankind at large because I feel like that is a story which has been done before (Contact, Close Encounters, Arrival etc).
The challenges they face within the microcosm of their journey are a metaphor for humankind.
The overarching conflict is the physical journey to witness the aliens, followed by the conflict between the boys faith and their religious upbringing, followed (in the background) by the conflict between humankind and its disagreements about what the arrival means.
Re-Draft 1?(Aliens not mentioned)
With their orthodox commune debating an apocalyptic fate, two rebellious boys embroil their indoctrinated friend in a perilous journey across the machine zone to falsify their faith and save their families.
Re-Draft 2 (Aliens mentioned)
As humankind grapples with the unprecedented arrival of an alien craft, two rebellious boys embroil their indoctrinated friend in a perilous journey across the machine zone to meet the vessel and save their strictly religious families from an apocalyptic fate.
Is the logline improving or am I just reorganizing the same adjectives and verbs?
Foxtrot25 was concerned with the lack of focus on the aliens themselves, do you think there is adequate conflict elsewhere in the logline to warrant investigation?