Having the same code in both the theme component and the plugin seems a little weird to me - IMO it would be better to decide between theme-component/plugin, and then go all-in. Overriding entire files isn’t something we do ourselves, and it’s not something we recommend. To override core/plugin behaviour, your theme component should use methods like api.modifyClass.
I suspect the root cause here is that plugin ES6 modules are prefixed differently from core/theme modules. Running this on your site, I see the modules are prefixed with plugin. I suspect if you enabled the theme component, we’d see another entry, but with a different prefix.
