I've been spending almost a week trying to fix this issue. I've been doing some hard surface modeling, cutting in various designs with difference and union boolean modifiers and it's gotten to the point it seems good to bake it to a low poly retopo. I've been getting issues from the get-go and while I've fixed it to an extent, some issues persist. Additionally, baking the diffuse (just the color, not the lighting), be it from selected to active or not, comes out as black every time.
Methods I've tried include:
Fudging around the order of the modifier stack. I moved some boolean modifiers and that seemed to fix some issues.
Triangulate modifier with the minimum threshold set at 5 or more vertices per face to prevent ngons. This seems to have allowed a lot more detail to bake through as opposed to before when it was full of ngons. I felt this was my best option as subsurf modifier made Blender grind to a halt.
Weighted normal modifier helped some of the shading, but otherwise didn't bring out the missing geometry.
Applied scale to every object in my .blend file, but everything seems okay.
I made sure the texture node is set and selected.
Below is the current resulting normal map I'm getting, and a screencap of the high poly object. The .blend file currently sits at 300kb, so if needed, I'll try to link that in a future edit.