Thanks for the cool project!

We have the same Epilog 45W laser at work, it cost 20 000$ and not 10k.
I might try that.

Here is a other idea for the programming header, hard to explain.
You could slide the PCB in the 6 pin header. So you would have 3 pin on the bottom layer and 3 pin on the top layer.
The 6 pin header would be exactly where you have your decoupling cap.
That would make the device longer/flat but not higher.

Thanks again!