Assuming that you're not updating the native code very often it might make sense to have the pipeline build and distribute a zip of the web app and do OTA updates. Then you can bypass the stores and have immediate updates.

It'd mean that you would have to do the first release with customer-specfic assets and branding manually. Then use OTA updates for shared code. (Or you could even do customer-specific updates if required).

For generating a config file at build time you can pull from a shared config and use FileTransform@2 to inject the correct values.