Looking at
https://deskthority.net/wiki/Matias_switch it seems like Matias used to have keyboards with clicky/tactile switches that used special linear switches for mode keys (e.g. caps lock) that used an in-switch LED to show which mode you were in.
Clicky/tactile switches can't have an LED due to the presence of a tactile/click leaf. However, I'm not sure whether the Matias linear switches (with red stems) can support an LED in the switch housing or not. In the specific section about Matias linear switches in that wiki, it says that they contain an additional leaf spring. I'm not sure if tactile/click leaf = leaf spring in terms of occupying the place where an LED would otherwise go. From the Matias site, they say: "With the Matias Quiet Linear switch, we've added a special internal leaf spring."
I'm guessing this does in fact take the space that could otherwise be used by an in-switch LED, but just wanted some confirmation if someone knows for sure.
Otherwise I'll just mount the LEDs on the underside of the PCB as the transparent housing encourages.