@car123 Your pin settings are correct for both configurations, you should not be inverting channels. Are you sure your pre doesn't invert channels, some do. In any case I doubt the inverted channels should be introducing any extra timing errors.
You need full burn in to properly evaluate which you seem to be aware of. 006 is easily more refined and musical vs 005 in my setup, I now consider 005 as slightly more on analytical side of neutral. Involvement with 006 was also slightly down on 005 for me until micro dynamics began to kick in sometime after 300 hours. Gaia kicked in nicely after around 200 hours, same with Tubulus cable. The 2M HDMI cable is likely producing needless timing errors, you're on right track with 1/2M, full silver wire I2S cable, no need to spend for the extra silver wire in an HDMI cable.
Keep us posted as sound develops.