Unfortunately… the simpler and more attainable solution is to just work inside the limits. Design to the working area, and learn how to use jigs to precisely place materials. A perfect example of this just came up with @Deleted and his cutting board project:
You can see another example of this alignment method in my map on slate project. While the slate fits in the workable area, I needed to center the engrave precisely and only had one shot at it:
You can use this method to engrave an item that is larger than the work area:
Any attempts to perfectly align your work across multiple steps will be met with a lot of misses, the laser is very precise, your accuracy will almost never match that. I find it a whole lot less aggravating to just stick to passthrough cuts and one-step engraves.