I prefer to set the grommets and trim into the file and save it. I use circles that are the same size as the piercing side of the grommet, it's pretty mindless at that point. Then it is easily repeatable without having to remember rip settings. Same with paneling, I just do it in Corel, it takes no time and 5 years down the road I can reprint a panel exactly the same.
In onyx it's super simple. I have a "banner" quicker - it adds 1" bleed, adds a line at the start and end of the bleed (fold line) and grommets every 24", with a holemsoze of .25". Super simple, nothing to remember and then you can just hit banner when you're ripping the file and it's all setup with literally no extra effort / time.
For paneling... We usually will panel in the rip. In onyx at least, it's easy to drag where you want your panels to be a d it'll auto tell you the size... So you can try to land each panel between text or easy to align areas. That's doable in illustrator / Corel.. but it's a bit more work.
We have our onyx printer folder synced to a local Nas. So all our pre flight / rip settings can be dropped back into onyx and it'll save a the settings - so if we need to reprint a panel... You just goto the Nas, grab the file, move it over and you can just drag it out of the queue. One more step than the way you do it, but it saves any color changes / resizing / etc.
And the biggest part... We have 2 latex printers, a solvent and a UV. All color matched and are pretty close to eachother... but I guarantee printing a panel from one to the other won't match, unless it was all pantones... and even then I'm sure it'll be slightly different. Being able to search for the file and see which printer it was printed on is convenient. We could just change the filename with the printer I guess - but this way cuts out that step.
Onyx is great for automating workflows, once we got used to using quicksets we've automated a ton of mundane tasks.