The lightning_rod.json file is the source of the error. The lightning_rod.png texture contains no specific texture for the bottom, so I suggest using the middle of the upper part's texture.
This can be fixed by replacing line 29 of lightning_rod.json with:
"down": { "uv": [ 1, 1, 3, 3 ], "texture": "#texture" }
Mycelium wasn't mentioned in the other posts so my search turned up nothing. Why are these blocks considered transparent? It doesn't make sense.
I just had a skeleton trap spawn on a mushroom biome where I had cleared the mycilium and replaced it with grass in 1.12.2
Also noticed dried_kelp_block has texture names dried_kelp_top and dried_kelp_side instead of dried_kelp_block_top and dried_kelp_block_side
Please update list
As of 1.13, all the log, stripped_log, as well as sandstone, red_sandstone, quartz_pillar, chiseled_quartz_block, and purpur_pillar don't have "_side" on the filenames like every other block that has a different top texture.
Can we bump this? I did many of the same steps as OP but agree that it seems to be an account issue. I had a LOT of entities loaded for a very long time and this begins my theory. I think having the entities loaded must have kicked me / caused an error on the realm instance/server which SEEMS to have resulted in my account being blacklisted from joining realms servers. My brother’s account works fine on my computer and network.