*Edited to delete Quote* -- I realized I replied to the wrong post!
You can change shine on the Advanced Materials Hud, but yes, the skin designers did create their appliers for the wrong layer. They go on the 2nd layer instead of the 1st. Whether it was the fault of the dev kit, or the designer, i'm not going to speculate. But I know Stray Dog did it correctly, and you can apply the Sepcular and Shine from the Edit hud to the skin. Other than that shine, glow, and tint can be adjusted in the Advanced Materials Editor for any layer.
Also, re: BoM Slink eliminated the alpha hud ... which makes little sense to me. Legacy's update to BoM was seamless, didn't even require an update to the body. Just detach the hud and reattach it, and BooM ... BoM. I know this is a body we love to hate, and I'm just as annoyed by the lack of transparency as anyone else. I hope I helped clear up some questions if they weren't already clarified.