If I understand the question correctly, I think you’d be better off hogging out the majority of the stock with a larger diameter bit and a relatively small overlap - just to speed up the process of eliminating the stock. Then run a more refined pass with a bigger step over and finally get those corners with your smaller bit. I think that will be the fastest course with the best result.
Also…watch your cutter height. 45mm down is a fairly deep cut…particularly if you have the original belted “Z”. Before I upgraded to the HDZ, I’ve had straight bits bind on withdrawal from pockets that are deeper than the cutting height of the bit - even though it was a straight bit.
I’d be interested to know if the box retains its shape after you cut it out of the stock. Depending on the wood type and moisture content, when you drastically change the shape of a piece of wood in a short period of time it has a higher tendency to warp. Going from a thick block to a box with a thin wall might cause that to happen. It is why the milling process (jointing/planing) in woodworking is usually done in several steps over a period of hours/days to allow wood movement to happen in between each step. That would be great if your box doesn’t warp as it would be a quick way to make a box and a great use of short cut-offs, which I have a ton of in my shop. I am definitely interested in making boxes on my Shapeoko and have been playing around with a 90deg miter bit for thin walled miter boxes with splines to strengthen the joint.