The bounding box is an odd number of voxels in each direction, yes. A core S is 127x127x127 voxels in size. That's a symmetrical space. This means that the central axes are aligned with the center of the voxel that's at the center of the build space. No idea what you mean by a "center" build guide, unless you're talking about the center of mass indicator, but that's a dynamic guideline. I'm also not sure what you mean by texture patterns aligning asymmetrically and "painted makes this obvious". If you want to make your ship symmetrical within the build space, just make it an odd number of voxels wide and align your elements accordingly. It's possible to do because elements snap to the edge and center of a voxel. I mean, I can see in the screen shot that the grid guides have "1 less" voxel on one side, but like I said in my original reply that just means the space is an odd number of voxels, that's not asymmetry. Again in the example of a core S you can build 63 voxels from the central voxel in every direction.
EDIT: Ok, so I figured out what you were talking about with texture patterns aligning asymmetrically, and what you mean by painted. And yeah, I can agree that is annoying, but it's not really game breaking. You just have to build your ship on an even center point rather than an odd one. The bounding box has absolutely no bearing on your ship apart from the size restriction, the game calculates your center of mass based on where your elements and voxels are placed. You don't even have to build from the center of the build area, you could build you ship in the corner of the build area if you wanted.
Beside that, I never use any of the painted voxels because they're all ugly AF anyway.