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Case for a genealogy system outside of Wikidata
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One case for not using Wikidata for Geneology would be that specific subtrees should be nonpublic. The present system prototype that builds on MediaWiki won't be able to answer that use-case.

Another case would be the desire to allow people to upload data that's not based on any sources. If that's the desire for the new project, then there's a completely unanswered question about quality control.

So, focus on coding something independent of Wikidata?

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Very good point about some subtrees needing to be private. The usual solution to this with MediaWiki is to have separate wikis for each group of users. This approach could work well with genealogy wikis too, I think — although, not, as you say, if the data is all on Wikidata.

As for quality-control, I think we should be aiming at a system that's easy for people to install themselves, so their unsourced content can be hosted away from the main central communal wiki.

The current prototype doesn't use Wikidata, and is mostly just focused on building the tree/graph of person-pages (and doesn't impose the family structure of Gedcom).

I may be wrong here, but doesnt different SQLs within Wikidata give a very useful and good way of keeping spcified records nonpublic. if this has been configured?

No, I don't think there's any way within Wikidata to make any records private. Perhaps there is in Wikibase (the extension).

A project to do this, which will hopefully eventually link with Wikidata, is History Research Environment (HRE): Developer support is most welcome!