The links in the principles give more details: https://malleable.systems/mission/#4-retain-ownership-and-co...
For this principle, it says:
>> "A fundamental problem of today’s software ecosystem is that we do not own or control the software that runs on our devices. In addition, much of the actual processing logic has been passed off to remote systems in the cloud, so only the inputs and outputs are observable."
>> "We must ensure that malleable software approaches allow the customisations and personal workflows you create to be owned and used as you see fit. If an approach relies on some amount of remote functionality (perhaps to assist with pulling apart an application or service), we must ensure there’s a clear path for anyone interested to keep those dependencies alive so that their workflows are not disturbed if the remote service were to shut down."
>> "This has many parallels with the ongoing movement towards data ownership, which is gaining popular awareness. Although the data ownership movement typically focuses on identity and social data, the programs and customisations that authors create are personal creative expressions. Authors must retain ownership of their data, programs, and customisations just as anyone would expect to have control over a book they wrote or art they created."
The first paragraph definitely matches up with your point that the user should be in control of their computing environment. However the third paragraph certainly seems like copyright and licensing are implied.