Sorry to take so long to respond to this thread. I've been busy with some other stuff. I think I figured out why imaging Sierra to High Sierra does not properly set the boot drive. If I run the command while booted into Clone Deploy (1.3.3) I get an error "Setting startup disk not allowed while System Integrity Protection (SIP) is enabled.
It looks like this command can only be used from the recovery partition. I can disable it before uploading an image and this fixes the issue with the ? boot folder. i.e. systemsetup is able to set the startup disk. However this leaves the device without SIP enabled which may or may not be detrimental to the final deployment (I'm sure Apple would view it as detrimental).
Of course it can be reenabled from the recovery partition. However I find it easier to leave it enabled and select Macintosh HD from the Startup Manager. Curiously enough this only happens when imaging from HFS+ to APFS (Sierra to High Sierra), but I bet that has something to do with the update to firmware since the setting carries over to the target machine.
Sounds great, I'm fairly busy with other projects at the moment but I'm hoping to start work on 1.4.x soon. I'm not looking to add much, there will be a new msi based installer for Windows. I really want to get all of the bugs worked out and documentation finished. Each page has it's own help section, many of which are still missing, if you want to create anything for those feel free. I know that some people criticize the getting started documentation saying it's not clear or missing info. If you would like to come up with something for that, it may be helpful for some. It's difficult for me to write the docs because I can't put myself in a new users shoes. I can set you up for wiki access if you want?
You are free to modify the boot menu as you want. CloneDeploy uses syslinux,ipxe, and grub, you would just follow directions for those bootloaders to modify the menu. In my experience though, most ISO's will not boot over the network because the entire ISO needs to be loaded into memory.
It's when using efi mode, in efi each partition and hard drive has a unique identifier, when doing a clone those identifiers are also cloned. When this is checked new values are generated. Generally this is not needed, but if you were to put the same image on two hard drives in the same machine, Windows would not be able to tell them apart with changing the values.