Good architecture starts with modularity
I know I'm too old to be agile and am insensitive to the Zeitgeist, but I got a distinct whiff of "Emperor's new clothes" from this interview.
We would then rewrite these queries into multiple queries that respect the domain boundaries and perform any necessary joins at the application layer
Nothing screams "modularity" like building a knowledge of your transient database schema into your applications.
For the foreseeable future we're going to remain with MySQL just because we have a lot of expertise there
If you had more expertise available with a database that facilitated doing joins across multiple data sources, you might not have had to build that into your applications. Shouldn't you be looking at the expertise you need, rather than the expertise you have, especially on a "foreseeable future" timeline?