Question: Will each instance try to run the same job
Yes! If you have 5 machines running the same site, they’ll all try to run the cron job. It’ll be inconsistent, but if machine 1 triggers WP Cron and there’s an event ready to run, and machine 2 triggers WP Cron, then machine 2 will also see that event if the timing is right and attempt to process it.
or will WordPress be able to resolve this so that each job is only run once?
Nope, it can’t. You can try adding a lock of sorts, but it can’t fix the problem, only prevent it in some scenarios
What you really need is to disable WP Cron in your config and run it via a system level cron job on a single machine. Or better yet, install a cron service such as cavalcade