This is just a rough idea. Perhaps someone could build from it.
It seems that many of the objects that I work on, have a series of boolean subtractions, which have to be performed in a certain order. In other words, it would like a boolean history object, kind of, in the spirit of a 2D vector program compound, such as Inkscape, Illustrator, or CorelDraw.
I wonder if would be helpful, the have the ability to designate an object as…um…compound or billet object. Once designated, the object is opened for adding objects to be subtracted from, such as bolt-holes pockets and so-forth, and these become associated with the object in a particular order.
When you are done, you close the object. The Booleans are done. Your subtraction tools are hidden. They move/translate with the object.
When you want to edit the object or it’s boolean tools, you click on Edit Compound. You make your changes. You might even see a list of them whilst editing.
When you are done, you clock on Close Compound Edit. The object is re-Booleaned, once again sort of like a History-Enabled object.
I feel that something like this would be a more natural way of work than say, another program I am thinking of that uses a non-contextual list of crap on the side, most of which the order of doesn’t really matter.
BTW, generally Rhino’s Booleans work pretty well. In many other programs, the users really hold onto a table or something, every time they do a Boolean.