The reason it is not working, and this does not just apply to my Optiplex 7060, but to a long of devices that the additional HDMI port is suitable for, is that the firmware Dell uses is based on a 2018 version of 11.116.000 (although if you read the firmware it reads as 11.116.101 )November 2020 and firmware update was released for the NCDP2900 chip that resolves, according to the release notes, audio issues on YAMAHA 2.1 receivers combined with TrueHD, Atmos, DTS-HD and DTS-MA  HBR audio tracks. This was version 11.116.010.The most recent version is firmware 11.116.014. Since Dell is using a custom firmware, with some tweaks to powersettings. They replicated the custom settings in the 11.116.014 firmware, which I then flashed onto the NCDP DP to HDMI chip on the additional HDMI port board and now I have the HBR passthrough working as expected.Dell, please use a more up to date firmware on this, still newly shipped, additonal HDMI ports, as specific features are known to be not working.My problem is resolved, but I do have a problem that nothing is done to resolve this for the greater public.
Although this MFF PC is out of warranty, it is perfectly capable and in good condition to run as Media PC. I have bought the additional HDMI port for optiplex 3060, 5060 and 7060 to add to the 2 DPs that the MFF has.The HDMI port works fine for image and standard audio. However, for audio passthrough it does not. it is connected to an HDMI 2.1 AVR, Marantz SR5015. The passthrough of audio (sending the audio straight to the receiver for decoding and not the OS) works for standard Dolby Digital and DTS, but not the HD streams. This is where the main benefit of passthrough is.For Intel NUCs there have been various HDMI chip firmware updates to resolve this issue. (I experienced the exact same issue on my old NUC with Intel 7th gen CPU which I flashed with a firmware that was designed for the NUC 8th GEN cpu, but I found out it had the same HDMI chip. )So it seems the Dell HDMI chip has the same problem. (Of course I did try to use the same firmware update tool on the Dell chip, but that does not work as it is not recognized as expected.)The HDMI port should support this as it is an HDMI 2.0 port according to the specs. Who has more info on the additional port for this system and a possible solution? It would be an absolute waste of fantastic hardware if we cant use these machines for this purpose. 
HDMI audio passthrough for HD formats (i.e. DTS-MA and Dolby TrueHD not working)