Thank you for the well made issue report.
While the missing shadows in the apitrace does indeed reappear when disabling ubershader the missing ship thruster effect seem to be a separate issue. I have bisected that one to commit https://github.com/doitsujin/dxvk/commit/3d2ee752b457fc79ff91f195975395e886f91d2a
This will need some testing:
SPECULAR_ENABLE controls whether the specular value is added to the final color in the pixel shader. This also happens if color1 comes from a programmable vertex shader. If the PS uses a color that either the FF VS or a programmable VS doesnt output, it gets 0,0,0,1, regardless of whether its color0 or color1.
It also controls whether the FF vertex shader actually calculates a specular color as part of the lighting calculation or just passes the vertex specular color (color1) along (default is 0,0,0,1).
The D3DTA_CONSTANT default is 0.
Setting the material source to a vertex color that doesnt exist in the vertex declaration makes it use the material color instead (like the documentation says).
As an update for @Cambidd because those last two comments were notes for myself more than anything else:
There's PRs up that fix both the thrusters and the missing shadows, so the game will be returned to all its glory. I expect them to get merged next week or maybe the one after that.
Fixed
Many thanks. Much appreciated.
Nothing extracted yet.
A number of shaders such as shadows for dynamic objects, jackal shields, covenant deployable cover, pelican thrusters, probably more, are failing to draw on the latest master.
2.7.1

2.7.1

Software information
Halo: CE (2003), Max setting.
System information
Apitrace file(s)
https://drive.google.com/file/d/1FmVzG58W9klQWSBF-TV0wV7woEDTQOq6/view?usp=drive_link
Log files
halo_d3d9.log