I'm a little unclear on what it is.. Did 'I' ruin something, or is this just a design flaw of the material itself.
And the only way to get rid of it is to "cover it up" by painting it?
Die cast metal I made by pouring or injecting molten metal into a mold. The mold in often heated so the metal doesn't cool too fast as it reaches all parts of the mold cavity. What you see on your bike is likely the beginning of a production run of parts where the mold likely wasn't at optimum temperature yet. The molten metal swirled around and when it met other swirls it joined, but was not the same temp, and that makes those ripple/imperfections in finished product. There can be internal voids (air pockets) this way that will weaken the final product. (So, they will often scap the first few parts out of the molding/ production cycle) Your sample was probably an early one that looked decent out of the mold. Further, some or all of those imperfections may not have even been visible, until you started removing the flash over metal hiding them. Since the factory painted them, they didn't leak, and weren't in a high stress area, you are probably the first to find those minor "flaws".
None of the metal on a bike is perfect, btw. You just can't see the imperfections that exist, surface or internal. You're polishing efforts have just exposed some cosmetic "flaws". It met original goals. Just not yours. So, it is NOT a design flaw. It is a process anomaly.
In a way, this is favorable to you, as paint will look far better for a longer period of time without frequent maintenance than polished cases will.
cheers,