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I take you start from the raspbian base image and customize your rootfs from there.

Maybe take a look at the various debian bootstrap methods then you can create minimal sd-images and even apply some changes to the root fs and partition table before booting the rpi.

This way you could implement encryption of the root partition or specification of partition size etc.

Here is one of the many bootstrap methods: http://liw.fi/vmdebootstrap/

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Exactly, I start with the Raspbian Full image and slightly modify it to work with PiBakery. If you want to see exactly what I have changed, I have a GitHub repo of that as well - https://github.com/davidferguson/pibakery-raspbian .

I will be doing the same process with Raspbian Lite (as having a minimal image is the most wanted feature) and allowing users to choose whether they want to use Full or Lite when writing to SD.

The problem I see is that this would work only with linux AFAIK.

Maybe cygwin can help here? Or run this stuff on a virtual system, vagrant, virtual box, qemu... I have no idea how to do this in windows/macos.

Or encourage your users to just ditch those proprietary systems ;)

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