You can talk to the System Boot Loader, via serial, USB, etc.
The protocols are documented, and you can implement in an OS / Language of your choice.
Problem is that they are designed for initial programming and recovery, and not really user friendly, nor protective of your code. Good for programming cheaply in the factory, and where engineers stand ready to resolve issues.
With your own loader you can use your own protocols, on pins/interfaces you chose, and in a manner that's secure and recoverable.
ie you can encrypt and sign the images, you can validate those before running, and revert to recovery mode if damaged or corrupt.
You can use common protocols like X/Y-Modem with assorted terminal apps, or your own apps that can connect via COM/TTY with relative simplicity.
With SD Cards you can deliver code/updates that way. With Cellular or Ethernet you can use network protocols, have code fetched via HTTP, FTP, or your own TCP/IP socket methods.
The system loaders are designed to be limited, and are not board specific. With your own you can use whatever features they provide. Typically you'd split the functionality in two, a loader and an application. The loader can validate the application, and you can add functionality based on how much flash you commit to each. Also often good to have storage where you can stage the entire update, that way you can ensure integrity before you start, rather than failing mid-way through the process.
A lot of this depends on your comfort level with the host systems your users expect. If you have to write your own device drivers that clearly complicates the task.
