Using the command line in Windows to create and individual zip archive of multiple folders.
Use case I have a directory with:

Which I want to make into:

You can use the following command, I am using 7zip replace with your archive tool of choice. This will create a zip in the root folder.

for /D %d in (.) do "C:\Program Files\7-Zip\7z.exe" a -tzip "" ".%d*"

Break down of command: for each directory %d is the variable and /D defines we’re looking at directories.
(*.*) defines the search location, root of folder your in.
do "C:\Program Files\7-Zip\7z.exe" a -tzip - 7zip command to add to a zip archive.
"" path of where you want the archive to be located.
".%%d*" defines the naming convention within the zip, this will have no subdirectory within the zip