Looks to me that Darktable only sees the Bottom layer. A multi-layer tiff is a bit like a PDF - opens in "pages" each layer a page.
Options:
Always save as a Gimp .xcf , a backup
Export as a Tiff with Save Layers OFF
Export with Save Layers ON but make a New-from-Visible and put that layer at the bottom of the stack.
Options:
Always save as a Gimp .xcf , a backup
Export as a Tiff with Save Layers OFF
Export with Save Layers ON but make a New-from-Visible and put that layer at the bottom of the stack.