You could do this when uploading by only selecting part of the data I guess.
You can do that of course!
I guess you could use a union backend so you'd upload a lot of files in a big zip (which you can still access individually) but set that as read only, so you would put updates in a new zip or a new directory. Not sure how deletes would work in that scenario.
If you want to have a go with the zip backend it is here: v1.58.0-beta.5990.02faa6f05.zip-backend
Use it like
rclone copy /path/to/files remote:file.zip
And read it back with
rclone lsf remote:file.zip
You can mount the zip, copy individual files out of it, etc.