I've updated my initial comments to reflect where I mis-represented things.
I'll try to move more detailed bug reporting to your actual system, but quick notes below. Also a reminder that I'm just one voice- what I say isn't law, and the way I expect things to work isn't necessarily "right". So long as you can get to the same end result, there's room for interpretation. It's when you literally can't do what you need to that there's a problem.
Adaptive doesn't clear outside stock, regardless of bounding box vs silhouette selection. This is with bbox (silhouette is even more constrained):
(you can also see it cutting a bunch of layers, when I'd really like it to do one depth on the outside and one on the inside- at least the option to control that)
Re AFR: This appears to be a different bug than I presented- it appears cuts you add manually subsequently show up in the AFR list- that caused me to believe it was partially detecting features, when in fact I had only partially selected them.
Re chamfer: The highlighted face is one giving me problems. There's no chamfer modeled on it- I just want to do a slight edge break. The entire contour has tangent end points- tiny radii in the "sharp" corners. If I select the face and try to chamfer, I get an error about the geometry. If I select auto loop, it only touches the outside of the "U" shape. I have yet to get manual selection to work- it's really tedious, and the couple times I've tried it's said it's an open loop and can't connect the edges.
Separate chamfer issue- maybe your fix mentioned above will correct it- but it's not just walls. In this case, trying to deburr (again, add a small 0.1mm edge break to the slot in the bottom) will run into the boss marked in yellow. This is one of the places where being able to adjust the start point would be helpful- normally what I do in these cases is to manually offset the start of the path to skip the area that's problematic.
Re lead-in/-out: This is more about options than operations that I saw that need it. There are lots of places where more control over the lead is required. Different leads for the lead-in and -out may be appropriate. Sometimes you want to lead in with a tangent line, not an arc. Sometimes you want an arc, but only 60 degrees, not 90.
New thing I just found: Pocket operation doesn't seem to respect the entry method for more than the first pass- you can see one helix entry, then a plunge on the outside pass. Doesn't seem to matter if I check the "keep tool down" box or not.
(this also illustrates a second thing I think is a bug- that green face is stuck highlighted, makes it hard to see the toolpaths)
And while I'm being picky... controlling the helix angle is important. Some tools choke at more than 1 degree, others are fine at 5 degrees.
OK, that wasn't that quick... but I'd like to end on a positive note here. Like I said in my initial post, I think the core looks really good here, and you're clearly dedicated to making things better. I really like to see that, and am optimistic you'll get there quickly.