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It looks like there's a hacky solution in #5633 but I agree, it would be really useful if there were even a simple extension template you could customise and build with a custom logo to add your own logo (and maybe introduce on-own-brand custom theme elements?)

Here is a related issue and PR from JupyterLite that seems to implement a custom logo: jupyterlite/jupyterlite#124 and jupyterlite/jupyterlite#130

It would be handy if there was a template extension repo for this sort of thing,

It looks like one way might be to create a simple plugin to add the logo, eg as per the default logo, but then you'd also need a way to disable or remove the default logo?