[robobass]

Robobass;
Two thoughts here:

You could use a manual rotary indexer and tail stock while still using a 3 axis mill and 3 axis software.

you can use the planar tool path near what you call the top of the part, and use Z level finish for the bottom few mm's.

Good luck.

I do plan on grabbing an indexer. A lot of the parts I make would still need the trough approach, though, and it's a gantry router without a terrible amount of Z height.

Yes, Planar on top and Z-Level-Finish on the bottom is what just I figured out and thought I was so clever. I was having trouble setting the Z range on the planar path, but finally got it worked out. I'm still having trouble with the planar sometimes cutting in air though. Not understanding that the roughing pass has already removed the material. Maybe I have to import a STL file for the stock.