Project export is not an option for archiving. Because of couple reasons. First of all, backup should be stored somewhere outside DSS which is not convenient. Export file could be lost, you need place to store it, everyone should have access to it and so on. Secondly, you cannot import bundle without creating a new project (correct me if am I wrong). So you have duplicate projects. Off course, you can delete old project and then import different one. But still that is not convenient.
Bundles were an option for this because you create a bundle and just switch between bundles when you need to change version. Not so nice as a simple git branch stuff but still it was relatively ok. But as we see, until it is ok only until the time when you need to migrate...
I understand that "bundle_activation_backups has no link with the project export or the design node migration" as you said.. But are you sure it does not contain all info about the bundles? I see all the recipes, datasets and other stuff inside those folders... Off course, I don't know what would happen if I just copy that to new instance. Unfortunately I don't have ssh connection to our servers to try it now.