No they should be different, they serve different purposes.
The user of the docs.hypha site will primarily be an adopter, therefore it needs to meet their needs first.
The hypha.app site could be used by anyone, therefore it needs to be a higher-level introduction to what Hypha is, what it does, etc.
Right now the hypha.app site is a 1 page static site, very simple.
I’ve created a site-map to map the information architecture of both sites.
@emlini if you create a miro account I can give you edit access.
Maybe the documentation index page should have even less of the “general” info it has now, and be more documentation-oriented.
Agreed.
What makes the most sense for users navigating to the documentation for the first time?
The documentation site should focus on Hypha documentation, with a short introduction para to give context to people who might find themselves there - “this is the documentation site for Hypha, the submission management platform for open funding calls…etc” - with a link to the hypha.app site.
In terms of the documentation structure, I’m not 100% but I’m sure you’ve got ideas! 
We already have a Github issue to for the hypha.app website: [Meta] Create Hypha product website · Issue #2164 · HyphaApp/hypha · GitHub
@emlini I’ve added a section called “Getting started with Hypha” and specifically linked to docs.hypha.app