I always use the top of the stock/material as Z=0. It looks weird in the layout assembly simply because the pieces are on top of the stock, but once you do a drawing from the top as a 2D DXF, it doesn’t really matter (makes it easier to see and avoid Z-fighting etc.).
All of the tool paths were created in VCarve from exported DXFs. I think I actually created a custom “form tool” for the bit I used in VCarve so that the previews would look accurate. You can basically create some geometry in VCarve that is a profile of your bit and it will simulate the cuts with a bit that looks like this.
The rounding bit tool paths were just small little straight lines. It actually got a little complicated to do that, because rounding bits don’t come down to a fine point, so I couldn’t just use the outside edge. Instead I think I had to copy all those lines and offset them myself. To put it another way, the bits have a flat part typically as can be seen on the second image of the bit I used: https://www.amazon.com/gp/product/B000P4LXSO/ref=ppx_yo_dt_b_asin_title_o02_s00?ie=UTF8&psc=1. Notice also how the radius is 0.25" on each side, the middle is 0.24", but somehow the total width is 0.75" .
I also feel like the arc in those bits drop a bit lower so I had to offset the height just a little bit. It was certainly a bit more trial and error via test fits than it should have been.