We would like to implement customized branding for the top navigation in the communication template based SPO site.
Can you pls share your thoughts and direction on how to implement.
For SharePoint Modern Site Branding, it is recommended to use SPFX solution to achieve:
And you could get started with SPFX from here:
In order to implement branding for Modern Sites, you need to implement Application Customizers. These will basically inject JS to your modern pages. As per your requirements which seems to be specific for Modern Communication Sites (SITEPAGEPUBLISHING Template) I would suggest to hold on till the end of August as the SPFx Engineering Team is releasing SPFx v1.6 which will have tenant scoped deployment. With this feature you can target your Application Customizer to point to all Modern Communication Sites (without the need to activate your solution for any specific site collection).
SPFx v1.6 Video
How to Inject JS using Application Customizer link