You can try using the Distance Sort option which will re-order the cuts by finding the next cut closest to the end of the current cut. It still could use some work to better optimize how it orders cuts for certain things at times but it can bring huge speedups.
There's definitely a plan to improve the rapid height when cutting where material has already been removed so that each rapid move doesn't have to be at the Safe Z height above the top of the canvas, but instead just a margin above the highest point along the rapid's path itself, or by using the state of the workpiece after previous operations - similar to how the Rest Machining operation works except that uses the simulated cuts to clip cutpaths against. I was thinking I could re-use that existing mechanism to implement a cut masking feature but it would use a designated raster or model layer instead of simulation heightmap :P
For projects like your ducky I tend to just let it rough out the corners and make sure my roughing operation is pretty fast, without a lot of long rapids (use Link Cuts), and then have my finishing pass come in with a Mixed cutting direction (when using the Parallel Carving op for instance) while also setting the Cut Depth equal to the Max Depth so that the cutter can reach all the way down in one pass - which can require that Ignore Tool Lengths is enabled if your cutter's flute length is shorter than the Cut Depth and just let it just cleanup the bottom of the pocket there around the shape being cut out. There's a bug in v1.53a that causes Ignore Tool Lengths to not properly allow Cut Depths that are larger than the cutter's flute length like it is supposed to - fixed in the next version - but in the meantime you just have to make sure your tool definition is long enough to accommodate it.
If you were to do a + or L shaped object that has a lot of empty space in the corners then it can definitely be a lot of extra time unnecessarily cutting them, and a legitimate masking feature would be nice to have for those situations :)
Charlie