How do you package Screen Savers for App Store submission?

That is not possible at the moment. As the author of https://EmojiSaver.eu I would like to see this as well.

Maybe the necessity for that will increase when there are some new Macs with OLED screens and they have to fight screen burn-ins.

Couldn't you encapsulate the screensaver inside an application with a .app file and set the screensaver from command line? How do you sell your screensaver online if there isn't an app store for it?

I bundled my .saver file with an app that opens the file on init, then exits. This asks the user to install the screensaver using Apple’s prompt. Apple rejected my app due to Guideline 2.4.5(ii). It states that apps “cannot install code or resources in shared locations”. Specifically, they said my app attempts to install a screensaver and to remove that functionality. It’s odd, because there are screensavers currently in the App Store. I don’t know how they distribute without installing the .saver

The screensavers I've found in the App Store are not .saver files. They are backgrounds where you can hide your desktop icons or standalone applications that become fullscreen when you open them. Distributing a .saver via the App Store doesn't seem possible at the moment.