This is something I find really frustrating in computing. We can do and are constantly doing such awesome and incredible things with computers. But at the same time transferring (copy-pasting) text from one application to another remains a challenge. And a reasonable solution for that is to bring in the 600lb gorilla that is a modern web browser to render fixed-width text into a bitmap so that it can be embedded into a presentation. It just feels so wrong, like the whole field is actually rotten inside under the shiny surface, while the state of the art blazes forwards thousand miles away from the real world. I, as a member of this community, feel utterly powerless to actually make the situation noticeably better, partly because of so much relies on interoperability, and partly because of the massive inertia that modern software carries.
Clipboards support storing different content for different MIME types at the same time. Atom would have to put text/html (or some other colored markup) in addition to text/plain into the clipboard and then Keynote would have to know what to insert. The infrastructure for interoperability is there, the endpoints just need to actually support it.
EDIT: Apparently, the problem is (or was in 2014) that Keynote doesn't support HTML and Chrome (Atom is Electron-based, right?) doesn't support RTF. Well worth a read: https://apple.stackexchange.com/a/124167
For code heavy presentations, I've seen a few people use Jupyter notebooks to solve this problem. Then just intermingle the rest of the presentation as markdown cells around the code cells.
Exactly, and to get the screenshot exactly as I want takes a couple minutes of setup – pick a theme, pick a font size, resize window – plus a few more if I have to stitch scrolled pages together.