I've been trying to bake some color masks into my diffuse texture in Cycles Render, and it generally works.
The problem is that the baked texture always looks completely different from the original, even when the only thing I connect it to is a diffuse or Principled BSDF shader. I'm using the Diffuse Color bake type (no direct or indirect lighting).
Original image texture (left) and baked image texture with only Principled BSDF shader (right):
I've circled and annotated most of the changes in the baked texture below:
a) The entire black area is gone and the dark and light grays of the diffuse bleed into it.
b) There is now some noticeable light grey patch in this area.
c) The once straight, linear edges in this section are now gone or heavily deformed.
d) The shape of the texture where the grey meets the dark grey is filled in and bleeds over another black part of the circled area.
e) The black portion is noticeably smaller and shaped differently.
f) There is no longer a straight divide between the light grey and dark grey in the circled area.
Here are my settings:
EDIT: I tried adjusting the margin from 16 to 4 pixels, but it seems like it's only modifying how much of the texture changes and cuts some parts of it out. Here's the baked texture with a 4 pixel margin prior to baking:
(Notice the green to red spectrum is cut off in the corner.)