Building a Sharepoint Intranet that's compatible with DM architecture

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I've been brought into a large organisation to help clean up their intranet (Sharepoint Classic with a Valo overlay). I was brought in chiefly on the content side, (I'm not a SP expert by any means). However it's now looking like the company wants to migrate all of the intranet to Sharepoint Modern with Viva Connect to provision. They want to do this as much inhouse as possible, so I'm trying to learn on the job. 

The thing that's challenging is this a really complex nationally run org, and their document management is all already in SharePoint modern. The DM has its own IA and navigational structure, with hub sites allocated according to business function. The IA isn't really fit for purpose for intranet navigation. 

Am I correct in thinking that the only way we can run a SP Intranet is if we rethink the IA for DM alongside it? There are NO communication sites currently, so we will have to build these. I was thinking we would need to reconfigure hub sites so that relevant 'Team sites' for admin, etc, can feed into the new hubs. OR, do we just create two separate SharePoint collections within the same tenant, one for the Intranet and one for DM, and just link between the two where necessary? I'm struggling to get my head around the architecture and requirements. Any thoughts or advice would be gratefully received! 

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