Ahsanallahu ilaikum, Ustadh, a man was driving and doing his job, there was no mosque nearby and it was raining outside. The Fajr time was going to end so he prayed in the car sitting. Is his prayer valid?

This depends did he actually did all the means to pray on time or somewhere protecting him from the rain. But if it was a dire situation and he wasnt able to pray outside then as sh salih alluhaidan said obey Allah to the best of your ability.