I think I figured out the folders aspect, and have reported this as a possible glitch in the very-complex interlocking and auto-self-modify behavior that goes on behind the scenes.
[BTW, the options in Decisions-Files > Folders regarding Source folders (including Create Folder on Source) are disabled during Modify for you because it is a Fast Backup profile, and we have to disable anything that might change the Source state after the Source state has been snapshotted as part of the Fast Backup process). The Modify process is common/generic, and doesn't know you plan to run a Restore next anyway. But it doesn't matter because once you figure out what is happening and side-step it - see below - the Automatic settings in Decisions > Folders work anyway]
If you Modify the profile beforehand to switch Decisions-Files, section-3 ('what to do about orphans on what is normally Destination (I)') from Delete to Skip, it should correctly propose to Copy To Source your empty folders during the live Restore (same as it does now in Simulated Restore). Naturally, this will stop it prompting during the Restore wizard about the de-orphaning aspect, because it's temporarily switched off anyway.
Doing it this way solves the issue for both Full and Incremental restores, because the behavior you're trying to suppress by agreeing to the prompt in the Restore wizard has been turned off 'at the fuse-box' c/o Decisions-Files anyway. Naturally, if you want to continue using the same profile for Incremental backups, you should change the Decisions-Files section-3 back to the Mirror behavior after all your Restores are completed.
[BTW, the options in Decisions-Files > Folders regarding Source folders (including Create Folder on Source) are disabled during Modify for you because it is a Fast Backup profile, and we have to disable anything that might change the Source state after the Source state has been snapshotted as part of the Fast Backup process). The Modify process is common/generic, and doesn't know you plan to run a Restore next anyway. But it doesn't matter because once you figure out what is happening and side-step it - see below - the Automatic settings in Decisions > Folders work anyway]
If you Modify the profile beforehand to switch Decisions-Files, section-3 ('what to do about orphans on what is normally Destination (I)') from Delete to Skip, it should correctly propose to Copy To Source your empty folders during the live Restore (same as it does now in Simulated Restore). Naturally, this will stop it prompting during the Restore wizard about the de-orphaning aspect, because it's temporarily switched off anyway.
Doing it this way solves the issue for both Full and Incremental restores, because the behavior you're trying to suppress by agreeing to the prompt in the Restore wizard has been turned off 'at the fuse-box' c/o Decisions-Files anyway. Naturally, if you want to continue using the same profile for Incremental backups, you should change the Decisions-Files section-3 back to the Mirror behavior after all your Restores are completed.