[Milhouse]

Is 3d frame packed supported on these builds?

Yes. Make sure you've enabled "Enable Full HD HDMI modes for stereoscopic 3D" and "Adjust display refresh rate to match video".

Despite having done both of these things, 3D .mkv files aren't playing in 3D on my RPi running LibreELEC 8.90.003 (Leia alpha 3) - is that a version where you'd expect this to be working, or is it only enabled in more recent nightly builds? (Is there something else I should check?)

LibreELEC 8.90.003 doesn't include any RPi specific Kodi optimisation patches at the request of Team Kodi - the primary testing focus for 8.90.003 is the OS, and not so much the apps such as Kodi. We hope to have found a workable solution by the time Kodi Beta 1 (8.95.001) is released, so that the end user experience is broadly similar to these test builds which DO include the full suite of RPi Kodi optimisations.