@mathieubossaert (and anyone else trying out offline tiles over Mapbox basemaps), offline raster layers are currently displayed with 50% transparency when using a Mapbox basemap whereas they are displayed with no manipulation with other basemaps. Which do you prefer?
I'm also interested in what @Ivangayton has to say. You described the "reference layer" as a "semi-transparent layer" here. I took that to mean that someone creating this layer will generally want to either use transparent PNG rasters or vectors with a style that doesn't fill everything in. Did you instead mean that ODK should take whatever file the user provides and render it semi-transparently?