There’s a lot to get into here and I’m not sure I understand it all. But I do have two thoughts:
First off, are you aware there’s a passthrough auto-alignment feature coming soon? It looks like the window for this beta cycle has closed, but keep your eyes on that thread in case more opportunities come up. Then, in regards to this:
If you are starting with a bitmap image, and you intend to engrave it, I would skip the trace entirely. This has the benefit of “what you see is what you get”, and avoids such issues as:
- Overlapping objects erasing each other (as you are experiencing)
- Having to do the right boolean operation to “knock out” parts of a shape
- Glowforge misinterpreting your SVG (such as even-odd fill rules, etc.)
In fact, I take this to 11. Even if I’m starting with a vector, I always rasterize anything I intend to engrave. This also gives you the opportunity to make one big engrave instead of separate steps, which may be faster depending on what shape it is and how much is empty space.