Hi again! I'm curious about your custom tool shape suggestion. Could you provide more details? What kinds of parameters or means of defining a tool are you imagining? A quick diagram would be great, or links to a few different cutters that you'd like to be able to define and perhaps I could come up with a means for users to articulate them to PixelCNC.
As for the tool holder itself: I do plan to show the actual holder/chuck for the very purpose you indicated, and also to perform automatic intersection tests to show the user if they might have problems with certain cuts that are deeper than the length of the cutter. This would basically operate the same way as the existing simulation system but almost as a secondary tool that's larger and at the top of the actual cutter, showing red areas wherever it "crashes" into the workpiece - which would be whenever the cutter has cut deeper than the distance from tip-to-holder. There's no telling when this feature will be in but hopefully within the next few months. The todo list is still rather long just to get us to beta but this is definitely a feature that's on there :)