I finally found the workflow.
Firstly I needed to create the scheme. I achieved this using the scene layer that contained both the "basemap" and my elevation, to be honest, I think none of the data in my layers mattered other than the extents and coordinate system of the map.
Steps:
- Generate Map Server Cache Tiling Scheme <- creates the first .XML file containing the tiling scheme.
- Generate Tile Cache Tiling Scheme <- Expand advanced options and select LERC compression in the Tile Format. For generation method use "predefined" and the output .XML file from step 1!
- Manage Tile Cache <- In Input Tiling Scheme use the tiling scheme from step 2. The output of this tool is a Raster Dataset that shows you the size and number of tiles.
- Export Tile Cache <- Export .tpk
- Finally, upload the .tpk from step 4 to AGOL using the add item, and check the publish box.
To add the correctly tiled map/raster on top of this:
- Same as the first step above
- Create Map Tile Package <- using .XML from step 1 (note, do not use the LERC .XML scheme from step 2)
- Same as step 5.
The .tpk does not contain information about the number of tiles or size. If you want this also for your tiled map/raster, I suggest you could do steps 1 through 5 but choose another Tile Format method, such as png/.jpg/Mixed, I have not tried this method for publishing the basemap, but I think it should work.