The variables are set in configuration files. Specifically configs/images/raspberrypi_raspbian_config. You can modify it there or add a local configuration file to override it.
We never modify the partitions in a live system. It’s not possible to do it robustly. We do have this link which is a method to do that but it can result in a bricked system.
mender-connect is a remote shell feature.
I honestly don’t know what will happen if you use the snapshot feature on a system without the dual partition setup. It may well create the artifact but you won’t be able to deploy it.
I’ll take another look at your converted image and see if I can find anything.
Drew