Some positive news. Reset the splitter and set it to 4k, and turned the HTPC on with the TV turned off, and now the passthrough options have returned and are working. Not sure if it'll survive a reset of the HTPC but its working for now!
Tried some samples with Atmos, DD+, TrueHD & DTS-HD and they all worked as expected.
Closing this out for anyone who finds this and has similar problems. The above solution didn't persist after a reboot. Upgraded the firmware on the splitter to v1.73 and that appears to have fixed the problem, has survived a reboot. EDID set to 4K rather than 2K or COPY1.