LX, at one time dropped their own flights GVA-LHR and code-shared on BA metal. While that arrangement disappeared long ago, the systems were integrated then, and nobody has wasted money de-integrating them.
I would not depend on two non-aligned airlines being able to issue through checked boarding cards, but that can happen.
I recall travelling AF or KL via their hub and was amazed that I could print a single boarding card for both flights! Haven't seen anybody else do that!