Hi,
Yes, it is in Google interests to show different and relevant sites to users.
You said, "2 websites for the same company (very different domains) - both sites are targeting the same primary keyword phrase, however, the user journey should incorporate both websites, and therefore the sites are very heavily cross linked - so we can easily pass a user from one site to another."
I am assuming the by very different domains, you mean different site address because two sites on two different topics can't be heavily interlinked. In this case, I would recommend to have a single website that is performing well in the search engine and merge the other one in it. As you said that users journey should incorporate both the websites, this means they are closely linked. In this case, it would be better to have a single website that suffice users' needs.
Regards