While experimenting with margins and such, I found a few places you could edit it.

You can modify it under Database -> Manufacturing or while manual nesting under View -> Properties.

I was under the foolish assumption that they may have really improved this software since 1998. Since I've spent most of my time on PM2000 (CAMduct's great great great grandfather).

I thought I could apply margins for each thickness of material, like ProNest gives you the ability to do. So while mucking about, I added a Global Variable to the tool settings of the machine. Turns out that overrides the nesting margin in the two other places you can set it. So now it's just a little vestigial box that means nothing unless you disable the global variable or change it there.

I'm told they're still developing the software but I'm not seeing much difference between them in the two decades between version. It's a little more polished. Crashes more. But there's some seriously silly oversights.

Just answering my own question for any other poor schmo who is having to learn this software in a high production environment and all the 20+ year veterans are reluctant to share their secrets.