From a quick reading of that page I think the LumoSQL authors are making the effort to maintain their set of modifications as some kind of patch which will continue to be compatible with future SQLite versions as they are released.
...which is exactly what you're doing when you branch off a release branch and start applying your own commits with no plan to merge them back to mainline.
> which it seems they don't want to happen.
They are already doing it. They are only arguing that they can reapply the same patches over the next release branch, but that doesn't really change anything.
If they want to stay as close as possible to upstream, you'd think they'd either keep it public domain, or else choose a public domain-equivalent license (such as MIT-0, 0BSD, CC0, etc).