Thanks for the feedback and ideas!
We know there is a bit of LED stray light going on. Some people like it as it reminds them of their backlit mechanical keyboards. But for indicator LEDs it can be suboptimal.
For the smaller 2x3x4/2x5x7 LEDs, a good technique we found was to use a piece of heatshrink tube. It's a great idea to roughen the top too if that is preferred. Sometimes you can also make the LED cloudy e.g. with acetone (nail polish remover) but needs to be tested.
For blocking the light from adjacent Matias switches, we have another solution in the pipeline (more info soon)