I have done something very similar with what you want to do using RGB 5050 leds. I had some clear Cherry MX keyboard switches that I wanted to illuminate and already had stock of the leds. So I made a footprint that had a hole in the middle the same size as the led with pads on the bottom layer. Then the leds were a push fit into the holes and i just soldered the led legs to the pcb pads.
If I remember correctly you cant put edge cuts on a footprint so I drew the hole on a user layer and then edited the file after to change them.
The yellow lines are the edge cuts
