Nice to hear that you are interested in speedrunning wildlands!
Although a video from both perspectives is preferred, it is currently sufficient to submit just 1 perspective. However when a mod can't verify that both players are in a loading screen the time will have to continue... so not submitting all perspectives might put you in a disadvantage.
Concerning the timer, for every run it is stated in the rules when the run/timer starts and when it finishes. For a coop run one can pause the timer only when both players are in a cutscene/loading screen. So when one is fast travelling and the other is still playing, the time will continue.
Good luck with ur runs! for further questions and information I would like to refer you to the community discord: https://discord.gg/hN9xExzk