tmanchiri

It also makes sense to me now that I didn't see the llama taking damage because the portal in the nether faces you towards the wall I built when you spawn so his head was probably in the wall

Now that you mention it, that is exactly what happened I think. I had a boat in the over world at a portal hoping to catch a pigmen if one wandered through. The boat disappeared (Or so I thought), I think it may have actually had a wandering traders llama get in it and go to the nether. When I went through the nether I heard a llama taking damage but didn't realize it was stuck in the bottom of the portal at that time. That nether portal I had built as a way to get back to our main city through the nether from a different city I was building at, so in the nether I decided to block one side of the portal ( as described in the report you linked) to make it obvious which way to walk to get to the next main hub portal. I tried repeating the effects by placing four more boats in the overworld in front of the portal, no more mobs ended up in the boats and getting pushed into the portal and the boats did not disappear on their own either so I am fairly confident a llama got through and died in the bottom of the portal. 

I tested more and it appears there may not be a bug, the boats were found within the obsidian on the bottom of the portal in the nether. I can only assume they were pushed through from the overworld by lamas or a wandering trader and then the boats clipped into the obsidian going unnoticed