Firstly, the log states that lighting flags are found and applied.
Secondly, I think I recall that Knossos will not work with pre-3.8.0 builds and has got none of these downloadable. This leaves you with 3.8.0-3 and all the nightly builds since then.
@Pacman110: You're basically using a default FS2 set of lighting settings... I suggest you to check out these: https://wiki.hard-light.net/index.php/Sample_Lighting_Settings
The thing with "blandness" and emissive lighting supposedly enabled is related to your ambient_factor: the value of 128 is horrendously high with the new renderer. Actually, I think it's the maximum value. For example, I like dark and shady views and I'm usually using the value of 73 or 75.
Ambient factor acts... strangely with these new builds. Up to about 70 it makes no change whatsoever, and above it it's a very steep line up to 128.
You can experiment with lighting yourself, there's an easy method. Just press F3 in the main menu, select a background (would be for the best if it was one you know), select a ship and then use the "Render options" menu to fiddle around a bit. It lets you check ambient, light from the suns and bloom. Find the values that make you satisfied and go with them!
For example, my settings: -ambient_factor 73 -spec_point 0.3 -spec_static 1.0 -spec_tube 0.3 -spec_exp 0.7 -bloom_intensity 35
HDR is one thing, the bloomy lights. But PBR, so the whole reflection handling system in place can simply be no longer controlled by one or two flags. I'm not a specialist on that but PBR basically lets the modellers handle how materials on their assets behave. So there isn't a way to use a general override for this - there's a map especially dedicated to handling this and the model/texture creator has to make it.
Gah, I think a SCP dev should answer you rather than me.