Google's John Mueller was asked if there is a Google SEO preference to having your structured data connected in some graph or node array versus having them as individual elements in their own blocks on the page. John said that Google has no preference.
This came up on Mastodon where Mike asked if Google has a "preference on the part of Google for using a graph array to contain / connect all structured data for a page in a single script block vs having individual elements in separate blocks?"
John Mueller of Google replied, "I don't think we have any particular preference in that regard. My general recommendation would be to focus more on the individual items that result in the type of rich results that you'd like to see. How you tie those elements together feels more like a theoretical question to me, it's (as far as I know) less critical for rich results."
So I don't think it matters or not, although some data geeks probably preferred everything tied up nicely in a bow...
Forum discussion at Mastodon.
Update: Ryan Levering from Google who primarily works on structured data said on Mastodon in response to this post that this is indeed true but there is a caveat. He said:
That's technically correct. Whatever the graph looks like for the whole page is what we use, regardless of where it comes from. It gets mushed together and while do know where it came from, that's not usually used.However, the caveat here is that when you do it in multiple blocks, there are sometimes conflict/duplication problems. Also, over time richer/correct semantics will favor more connected graphs. We still see cases where people throw unrelated markup about things (like related products) at the same top level as the main entity from different blocks on the page and that makes it mostly noise. So sometimes centralizing the logic makes it more consistent/correct. Just use a tool to preview it to make sure it says what you want it say.