Creating a new world, and putting in a datapack (that has more than 3 namespaces) inside removes those folders before uploading to Realms. It seems that it always keeps the first, last and minecraft namespace (alphabetically) when it's on the Realms server.

World download with datapack: https://www.dropbox.com/s/xpr7xjftala69vt/Separate%20Datapacks.zip?dl=0