I just thought I’d post an update on my new computer: it’s been assembled, it’s been shipped and it’s due to arrive here this Wednesday. I can’t wait!
Meantime, I was looking into what was going wrong with my GeoPackages, and I found out that there are problems with (my now slightly outdated versions of) QGIS and Spatialite that prevent GeoPackage spatial queries from working. So it wasn’t me!