There's no POI subfolder contained in .System folder. It's a root folder, just like .System is. I'm not sure what would have been copied with the command you wrote (copydir,0:/.System/POI,1:/.System/POI) but likely it'd ignore the POI following .System in the first part of the command and try to copy the entire onboard contents to the target path you specified with misnamed or nonsense folders and with random files scattered all over within the subfolder "POI" of the newly created ".System" in the card's root.

The correct command to copy only the POI folder contents should be this:
copydir,0:/POI/,1:/Backup
Although you can name that target folder on the card anything you like, e.g. "POI", "POI_Copies" or "GPI_Files" or even just write "copydir,0:/POI/,1:/" and then a copy of onboard POI folder's file content will appear in the root of the card.

You can make a fake device by using a suitably sized USB stick or media card formatted in FAT32. Make a root folder named Garmin on it. Place into that folder the GarminDevice.xml file from the device. MapSource should recognize it as the device itself and transfer data to it as if it's the actual device. NOTE: Avoid using MS to create NT/NTU .img files or you'll quite likely get navigation errors and random re-booting or freezing of the device. Use only MapInstall for that purpose. MS is old and unsupported and deals with PC Data using an outdated algorithm that cannot properly process a lot of modern .gmap data into .img files. It's quite safe to use MS to transfer other data however.