I had a thought that maybe using Difference instead of Union would help with this problem. Probably not, but worth a test. But before I got to testing that, I had yet another thought
In the attached file, I recreated that original design that I made before. I made it in 2 different ways. The way I made it originally is in Layer 2. In Layer 1 is the step just before we get to what's in Layer 2. I wonder if Blender can accept the drawing as in Layer 1?
In Layer 1, everything is still a stroked path. In Layer 2, I used Stroke to Path, and now it's a filled path with no stroke. But I just had the thought, that maybe Blender can accept the stroked path, and maybe it has a better way of converting it, to avoid this problem? Then Blender does the conversion instead of Inkscape.
Lazur can probably answer that as well?