It would help if you did post detailed photos. You said patches, which makes me think of handling errors.
In general, there are multiple reasons for uneven dye penetration (freshly anodized surface is porous until sealed, and that's where dye penetrates). One could be that people at the anodizing shop handled the case, between anodizing and dying, which can result in fingerprint marks and blotches where the case was touched. Another reason would be uneven anodizing thickness, which is a factor of finish and whether the case was dipped uniformly in the the anodizing bath. Re-anodizing repeatedly can wear out the original finish texture and result in some things like those horizontal lines. My LZ-GH case has been re-anodized a couple times, with an acid bath eating away the old anodized finish in between, and I can see those lines at some angle along the sides. They are possibly from the original CNC cutting or the way the alloy microstructure happens to be. I've handled another reanodized LZ-GH, and that one too had some faint horizontal lines around the edges, which reinforced that idea. So this is not something to do with the case being cheap. If you want top notch anodized finish, the surface needs to be prepared afresh (like bead blasting) and then anodized and dyed uniformly. Otherwise these problems with uniform finish can arise.
(On top of that, I've read a bunch in the past about people doing their own anodizing, and they frequently shared that some dyes worked better than others for them or were more or less temperamental in terms of water temperature and pH. Presumably your shop knows about it already, but could be the case that the dye did not penetrate uniformly and well enough).
I don't know about the processes described in on the page you've linked to--I'm not a material science specialist--could be additional factors at play of course, such as uniformity of alloy composition and such. But the fact that you got the case in a uniform color and then re-anodizing made the result non-uniform, I'd consider checking how the shop removed the original anodized layer (whether it was sufficiently well removed), how well they left the dye penetrate after anodizing, whether they handled the piece in between.
