TLDR: Transparent keys are keys that you can assign in a layer ( e.g. layer 1 ) which instead of doing nothing will inherit the functionality of the previous layer.
E.g. If you set the WASD keys as transparent in layer 1, then any time you change to layer 1 using FN1, all keys will change except the transparent ones. Those will continue to function the same exact way as the main layer, both including the mapping but also including settings such as actuation points. This allows you to, for example, switch to layer 1 and press a key from it without losing control over your character in a game, because WASD are still available.
This is currently achievable, if you copy over the configuration for the keys from the main layer to layer 1, but this isn't synced up. So if you change the main layer, you have to remember to change layer 1 to match. Also, you have to do this for each profile individually instead of relying on the layout linking in the Remap tab. Transparent keys will solve both of these problems.