In the Burner Furnace the Krastorio 2 Loader it wont take out the Ash at all.

That is true, loaders cant unload from burnt inventory like the used up uranium fuel cell. the miniloaders mod would work for this.
Normally that fine but for the burner furnace this will be inconvenient.

I seems like I do need to use my idea from: https://mods.factorio.com/mod/Seaworld/discussion/65c1bf722757e859c134bda5
Sadly that will replace the furnace with a different entity with another type. hopefully migration script can handle that but I am not sure.

Will look into it when I can.

i cant say i have personal experience with migration scripts but in theory, as long as it has the same size you can just replace every entity on the surface with the new one and set some value thats stored in the save game as the toggle if the mod should disable the old entity or not and also disable the recipe to produce it and replace any already existing items in inventories with the new one.
i think what someone else did also was if you cant just slot it in the same place to give the first player who joins the safe on the same force that owns the entity just a replacement and they can put it down them selfs if they have to re design anyways.
however it would probably require to permanently keep the script in case someone skips some versions in updating or give a warning for people to download a specific version first so the script can run and then update to newer versions if a newer version is available.

I did it, the new version is available here: https://github.com/Rebecca-kve/FactorioMods/tree/main/Seaworld_0.1.8

Burner furnace can now use loader, and conflicts with space exploration has been resolved.
I will update tomorrow here on the mod page
multiplayer is still untested