Vagrant / Packer?
For data sustainment if they need to upgrade / replace VMs, have a secondary EBS (volume) mounted which solely stores persistent data for the account.
1. Start a base image of Debian / Ubuntu / whatever – this is often done with Terraform.
2. Packer types a boot command after power-on to configure whatever you'd like
3. Packer manages the installation; with Debian and its derivatives, this is done mostly through the arcane language of preseed [0]
4. As a last step, a pre-configured SSH password is set, then the new base VM reboots
5. Ansible detects SSH becoming available, and takes over to do whatever you'd like.
6. Shut down the VM, and create clones as desired. Manage ongoing config in a variety of ways – rolling out a new VM for any change, continuing with Ansible, shifting to Puppet, etc.
I think I'd usually rather just use whatever distro-specific tools for putting together a li'l chroot (e.g., debootstrap, pacstrap, whatever) and building a suitable rootfs in there, then finish it up with amazon-ec2-ami-tools or euca2ools or whatever and upload directly. The pace of iteration with Packer is just really painful for me.
If you dual-boot multiple Linux systems you can still administer any of the ones you're not currently running via chroot at any time, and that works fine whether you've got third-party repositories or not. A chroot is also what you'd use to reinstall the bootloader on a system where Windows has nuked the MBR or the EFI vars or whatever.
There might be some edge cases like software that requires a physical hardware token to be installed for licensing purposes is very aggressive, so it might also try to check if it's running in a chroot, container, or VM and refuse to play nice or something like that. But generally you can do basically anything in a chroot that you might do in a local container, and 99% of what you might do in a local VM.