They absolutely have left that door ajar on purpose. Presumably they calculate that by being the de facto go-to reader for the people who want to install their own software, they can both sell more devices and don't need to splash a lot of money up the security wall playing cat and mouse with motivated hardware hackers (who would become pretty motivated if they found there were no open platforms). It's not as if people who would install koreader would just roll over and start throwing money down on Kobo store books. They'd just never buy a Kobo at all.

I have a Clara HD and it's a fun little Linux device (no android nonsense, just a good old shell), Koreader is pretty great (a few rendering bugs aside) and I can even ssh into the thing _and_ pull files down from my computer with WebDAV though the koreader UI.