Disk Utility of 10.6.2 install disk does not recognise SDD; Disk Utility of El Capitan does
I solved the issue by installing El Capitan on the USB (via another Mac) and booting from there (a full install, not just a boot disk). The El Capitan booted from the USB did see the SSD, so I could install El Capitan from the USB onto the SSD. 

The core issue was that Apple seems to have added third party SSD support after 10.6, so installing 10.6 was never possible.