Don't know what anyone else's experiences have been with this but it's something I've had quite a few headaches with. I have two sites that run local backups every evening then do a backup copy job to each other, then I also run frequent backup copy jobs to disk. So far so good, nice maintained single job for each vCenter site, nice single backup copy job per destination. Fast forward about 6-9 months and inevitably there's some problem because stuff happens, either an unscheduled power outage occurs or the site to site link went down mid backup copy job, next time it runs I get a couple of VMs complain about corrupted restore points as they were being worked on at the time. The only solution I've been given from Veeam on this one is to do an active full of the VM backup copy that failed, it makes sense however you can't do it within the backup copy job without performing an active full for the entire job.
I'm then advised to split out the troublesome VM from the core job and make it its own. This by itself isn't a problem, but by the time you've had to do this for a bunch of VMs over time you end up with dozens of separate jobs. It'd be great to add a folder structure to the Veeam B&R application so I could then just preempt this with every VM as its own job, grouped into "site A to B" folders etc.
I backup all my VMs to separate backup files to increase the resiliency and use them alongside scale out backup repository to minimise damage when the inevitable does happen (that's why we have the 3-2-1 rule right?) but the organisation of these jobs has become very messy over time.