Why are there some packages in the Software application but not in apt?

You have just discovered "snap" packages, they are deployed by "snappy" package management system built by Canonical Ltd. (the Ubuntu company).

Snaps are containerised software packages that are simple to create and install. They auto-update and are safe to run.

Read more here: https://docs.snapcraft.io/getting-started/3876

The Software application also contains snaps, in fact

Some applications are available in both formats. In such a case in Ubuntu Software the snap will be listed first. (source)

isn't the software center a graphic interface for apt

No. Ubuntu software center also supports snap installation. See the snapcraft store. Discord on command line would be

sudo snap install discord

and atom would be

sudo snap install --classic atom