At first I read your post and thought “yeah, that could be useful!” but, then I thought about the other risks and issues that it would introduce—it would probably need to be introduced with a group of additional features, which could get to be substantial feature creep…
For instance, if you replaced the tool with the exact same tool, and had it adjust the length by the new measurement, then the net result will be that the tool takes the same tool-path—which doesn’t necessarily solve the reach problem you encountered, as the end-depth of the cut will be the same. The only thing it will have prevented is collisions with the collet-nut, and it didn’t sound like that was your main issue here.
What you’re looking for is a way to have an additional z-height compensation that can be applied at the Carbide Motion level instead of in CAM, but how would you then ensure that your feed-rates are appropriate for the adjusted cut-depth, and that you won’t accidentally jam the cutter into the material too deeply? Or if the tool is lower then when the spindle retracts to go between areas in the part are the retractions still going to pull the tool high enough? If the tool path is being executed at a lower z-height overall, then it’s going to introduce all kinds of new opportunities for “whoops!” without the benefit of a simulation to preview the impact of the changes, like you would have otherwise in MeshCAM or other CAM packages.
Generally, since you program your stock dimensions in accurately prior to generating tool-paths, and then you set your zero positions prior to running the job, that’s when you’ll be ensuring that the tool is going to travel where it’s expected to on the z-axis. The critical part here is setting and checking your zero positions before the job—if your z-zero is floating above the stock, then it’s going to cut air first instead of your material, and then the bottom of the cut won’t be as deep as you are expecting, as you experienced X-)
But, I do think it would be a value-add to have a check of “overall length” and “flute length” of the tool as provided by MeshCAM, or “Body Length” as provided by HSMworks/Fusion360. That would be the opportunity to account for and prevent potential collet/stock collisions.