Zero tool at tool change

So I have been using Fusion360 for my CAM. It uses basically a dumbed down but growing version of HSMworks.
My machine is a small home built machine using an ER20 collet so I need to rezero the machine for each tool change. Simple enough, in CAM I just create a setup for each tool.
If it helps, you can see how this all works in F360 here. Setup starts on page 11.
myhub.autodesk360.com/ue29c9141/shares/p...761eaa673e8e12d8f6b4

Now this worked quite well until they finally implemented patterning. Their implementation really frustrated me because a pattern is a child of a setup so for me I would have to create a pattern for each setup.
So for example for me drilling with a 3mm drill bit would be a setup, then all holes with a 4mm bit would be another setup, facing with a face mill would be another setup and pocketing would be another setup.
I am of the opinion that a pattern should be a parent feature or separate feature that can be applied to any setup.
At that point I was told that I am using the CAM wrong and that all operations for a given orientation should be under one setup. I told them that didn't work for me because I had to zero my tools each tool change. They then made it sound like that should be easy to do during a tool change. As far as I can tell this is not possible in Linuxcnc. Is there a way to do this?

Thanks for the input. My collet doesn't have anything mechanical to set the height.
Some of my cutters and drill bits are also shorter than the length of the collet.
Integrating a step or other stop into the tool is an interesting idea but the thought of doing that on all my tooling especially things like very small drill bits seems less than ideal.

The software solutions you mention still leave the issue and question of how to do it during a tool change.

Whether I zero off a touch off fixture, the part, the machine, the vice or whatever else I would still need control of the machine to do so yet when time for a toolchange comes in Linuxcnc it disables the machine, asks you to insert the next tool and then click okay. As soon as you do then it takes control of the machine again.
This brings me back to my question of whether there is a way to zero the machine during the toolchange?

I would really love to do an automated touch off plate. If you could go into more detail on how to set that up in linuxcnc I would be stoked.
Even if for now I could get control of the machine and use a similar plate to manually zero that would be helpful.

I skimmed over it quickly. Will look at the config next time I am out at my machine.

In the meantime what is the best hardware setup?
Would I need to make some sort of spring plate or something with a little give to it so the cutter didn't slam into a solid surface?
Would I use something like an estop switch? Or insultate the plate so touching the tool completes the circuit?

Wow thanks. I didn't even think to look for these. i figured it would be more of a high end item.