Well….I’ve figured it out.
Manually deleting everything in Crontrol didn’t help as much as I thought it had. I went to my wp_options table and deleted the entire cron entry. On refresh now, everything looked more or less how I expected, and all of my questions are answered now.
When disabling WP Cron to enable your servers cron, the timing on wp_scheduled_events is not forgotten. If you call the file and the job still has 30 minutes left before it should be run, it will not be run. Therefore, there is no benefit to calling the cron job more often than your minimum timer. If your shortest timer is hourly, and you’ve disabled WP_CRON, don’t set your cron to less than an hour!