Hi @sBerguiga
As you say, the marketplace Pandadoc integration doesnt support custom objects. Unless they add this functionality, you are going to need an alternative or custom solution.
By alternative, I mean that you could perhaps look at using workflows to pass the relevant information from the custom object to a standard one (contact, company, deal) before creating the pandadoc doc. This may or may not work for you depeding on how you are using custom objects.
The custom approach is to develop a custom API integration between the two systems, either from scratch or potentially using a low-code integration platform in middle.
Hoep this helps?