Hi!
The benefits of having it in one instance are huge imho. Our community exists and knows how to handle structured data by now. Processes/documentation/etc are set up. The world outside is starting to realize that Wikidata is the place to go to for structured data around Wikimedia now. And we probably do want easy connecting between
All this is true, but I don't see why this implies running only one instance of wikibase. We could run another instance under the same Wikidata umbrella, connect them (just as we are connecting other wikis with Wikidata), share relevant documentation, etc. - neither of that mandates running everything within the same database. I think we have a lot of experience here of running services that are different technically but unified by common goals and common purposes and linking them.
items/properties/lexems etc. As we're talking about different entity types the data is easy enough to keep apart for those who want to.
I'm not sure how easy that would be - I've seen a lot of code that assumes certain things work with all entities, now this code needs to be reworked to work with only two types of entities, or support many other types that behave very differently. And it's very easy to miss something and not discover it until we launch it and tools start to break because Lexems get into code that assumes something is either Item or Property. And I'm not talking about internal PHP code only - there's a lot of tools out there that neither WMF nor WMDE maintains. It's one thing to make new service (which btw I think is an awesome idea, just wanted to say it so that it would be clear than I am not criticizing the whole idea, just this aspect of it) and another add subtle changes to an existing one.