The camera’s alignment is never going to be 100% accurate. You don’t want to have to depend on it for aligning a cut.
You can include both the cuts and engrave in the same SVG file. When you pull it in to the GFUI there’ll be two tiles in the window on the left (because cuts are vectors and engraves are filled objects or bitmaps, so it can tell the difference). When you hit PRINT the GF will perform the operations in the order they appear in that window. You can drag to rearrange the tiles to change the order. Alignment won’t be an issue because you won’t need to touch the part between cutting and etching…
Each unique color or layer or image type (vector vs. raster) in the source artwork will appear as a separate tile in the GFUI.
If this doesn’t address your problem, maybe I’m not understanding your question correctly?