I just tested this out on one of my appliances, and had the same issues when I tried to follow the Maintenance Plan wizard.
I'm not sure of the issues you mentioned above, and would like to research it further. Can you open an SR (PM me the SR#), so I can get the work into my queue to get done.
Just thought I would weigh in here. Part of the appliance setup is hardening and disabling of certain items which could be compromised. So to answer your questions:
1. Yes, any appliance will be setup in this same manner
2. The changes to the agent service would be the most preferred method, but it does alter the hardening of the appliance. Other automation solutions would require installation of client software onto the appliance which is not recommended.
3. As this "breaks/changes" hardening I am not sure we would want to add it to the standard documentation, there could possibly be a KB article written for registered users. (This is the question getting Cathy an SR for would be most beneficial)
4. Impact should be minimal, although if you have a number of transactions occuring at the same time as your scheduled backup this could cause deadlocks, slowness, or other unusual behavior. My suggestion would be if you are scheduling automatic backups, to do so when you have the least amount of scans occuring.
Submitting a SR and getting it further researched in support is never a bad idea, hope this helps.
Quick update on this. https://kc.mcafee.com/corporate/index?page=content&id=KB73630 (available to non-registered, I just checked)
Note that the KB does say this is a supported configuration, but Daves comments above regarding scheduled backups should be followed! Cheers for all the assistance with this Cathy!