Originally Posted by
Trenloe
This is because modules aren't created using the layer extension, so pins are automatically stored on the default, single layer which is the bottom layer. This is mentioned in the "things to note" list in post #1:
The extension can't change this as there are no FG API calls available to change the image (layer) that a shortcut (pin) is on. There is an API available to allocate the layer a token is going to be placed on (as part of the encounter token placement process) and that is why tokens from an encounter appear on the top layer.
All of the gotchas/things to note listed in post #1 are primarily due to there not being an API the extension can use to change an exception/different functionality, or the only reliable way to do something with multiple image layers.