/etc/ssh/ssh_known_hosts is labeled as a synced preference in the options page, so if you change it, the settings show up on all systems.
to be clear, this only affects the extension. there is no way for the extension to read/write system or user files.
(i mean, it could be implemented to a degree, but it's really not worth the hassle, nor the terrible UX.)
so if you're asking how to sync settings between native `ssh` run on your system with the Secure Shell extension, the answer is "you have to do it by hand".